SDHB

gene
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Summary

SDHB (succinate dehydrogenase complex iron sulfur subunit B, HGNC:10681) is a protein-coding gene on chromosome 1p36.13, encoding Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (P21912). Iron-sulfur protein (IP) subunit of the succinate dehydrogenase complex (mitochondrial respiratory chain complex II), responsible for transferring electrons from succinate to ubiquinone (coenzyme Q). It is a selective cancer dependency (DepMap: 45.1% of cell lines) and haploinsufficient (ClinGen: sufficient evidence).

This tumor suppressor gene encodes the iron-sulfur protein subunit of the succinate dehydrogenase (SDH) enzyme complex which plays a critical role in mitochondria. The SDH enzyme complex is composed of four nuclear-encoded subunits. This enzyme complex converts succinate to fumarate which releases electrons as part of the citric acid cycle, and the enzyme complex additionally provides an attachment site for released electrons to be transferred to the oxidative phosphorylation pathway. The SDH enzyme complex plays a role in oxygen-related gene regulation through its conversion of succinate, which is an oxygen sensor that stabilizes the hypoxia-inducible factor 1 (HIF1) transcription factor. Sporadic and familial mutations in this gene result in paragangliomas, pheochromocytoma, and gastrointestinal stromal tumors, supporting a link between mitochondrial dysfunction and tumorigenesis. Mutations in this gene are also implicated in nuclear type 4 mitochondrial complex II deficiency.

Source: NCBI Gene 6390 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): mitochondrial disease (Definitive, ClinGen) — +9 more curated relationships
  • GWAS associations: 24
  • Clinical variants (ClinVar): 1,581 total — 189 pathogenic, 65 likely-pathogenic
  • Phenotypes (HPO): 214
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 45.1% of screened cell lines
  • Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_003000

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10681
Approved symbolSDHB
Namesuccinate dehydrogenase complex iron sulfur subunit B
Location1p36.13
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000117118
Ensembl biotypeprotein_coding
OMIM185470
Entrez6390

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 9 protein_coding, 6 nonsense_mediated_decay, 3 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000375499, ENST00000463045, ENST00000466613, ENST00000475049, ENST00000475506, ENST00000485092, ENST00000485515, ENST00000491274, ENST00000714029, ENST00000714030, ENST00000714031, ENST00000714032, ENST00000714033, ENST00000714034, ENST00000714035, ENST00000714036, ENST00000714037, ENST00000714038, ENST00000925621

RefSeq mRNA: 2 — MANE Select: NM_003000 NM_001407361, NM_003000

CCDS: CCDS176

Canonical transcript exons

ENST00000375499 — 8 exons

ExonStartEnd
ENSE000035982391703306017033145
ENSE000036817431702860017028736
ENSE000037282851704476117044888
ENSE000037869141702774917027865
ENSE000037915781702397317024074
ENSE000040139031702260817022730
ENSE000040225841701872217018958
ENSE000040225951705394817054032

Expression profiles

Bgee: expression breadth ubiquitous, 293 present calls, max score 98.96.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 75.8158 / max 515.5937, expressed in 1827 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
1056964.97301826
105706.28621735
105714.39621668
105680.137571
105670.01672
105660.00622

Top tissues by expression

295 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
heart left ventricleUBERON:000208498.96gold quality
cardiac ventricleUBERON:000208298.94gold quality
apex of heartUBERON:000209898.88gold quality
gastrocnemiusUBERON:000138898.82gold quality
hindlimb stylopod muscleUBERON:000425298.82gold quality
mucosa of transverse colonUBERON:000499198.80gold quality
muscle of legUBERON:000138398.71gold quality
heart right ventricleUBERON:000208098.71gold quality
right atrium auricular regionUBERON:000663198.67gold quality
muscle organUBERON:000163098.59gold quality
right lobe of liverUBERON:000111498.54gold quality
heartUBERON:000094898.49gold quality
vastus lateralisUBERON:000137998.45gold quality
biceps brachiiUBERON:000150798.45gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450298.45gold quality
rectumUBERON:000105298.44gold quality
cardiac atriumUBERON:000208198.44gold quality
body of tongueUBERON:001187698.42gold quality
diaphragmUBERON:000110398.28gold quality
quadriceps femorisUBERON:000137798.23gold quality
skeletal muscle tissueUBERON:000113498.20gold quality
transverse colonUBERON:000115798.20gold quality
right adrenal glandUBERON:000123398.03gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451198.00gold quality
left adrenal glandUBERON:000123497.95gold quality
left adrenal gland cortexUBERON:003582597.87gold quality
right adrenal gland cortexUBERON:003582797.87gold quality
triceps brachiiUBERON:000150997.85gold quality
body of stomachUBERON:000116197.79gold quality
jejunal mucosaUBERON:000039997.73gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-CURD-11no380.49
E-MTAB-6524no228.89
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AHR, HIF1A, NFE2L2, NFYA, NRF1, PLAGL1

miRNA regulators (miRDB)

44 targeting SDHB, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-428299.9975.366408
HSA-MIR-314899.9775.066478
HSA-MIR-448799.9664.581252
HSA-MIR-55999.9572.283609
HSA-MIR-548AB99.9571.313488
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502
HSA-MIR-548AK99.9471.243488
HSA-MIR-548AM-5P99.9471.243488
HSA-MIR-548AP-5P99.9471.143489
HSA-MIR-548AQ-5P99.9471.343426
HSA-MIR-548AR-5P99.9471.283515
HSA-MIR-548AS-5P99.9471.223482
HSA-MIR-548AU-5P99.9471.243488
HSA-MIR-548AY-5P99.9471.233502
HSA-MIR-548B-5P99.9471.233502
HSA-MIR-548BB-5P99.9471.273509
HSA-MIR-548C-5P99.9471.243488
HSA-MIR-548D-5P99.9471.233502
HSA-MIR-548H-5P99.9471.243488
HSA-MIR-548I99.9471.253481
HSA-MIR-548J-5P99.9471.143489
HSA-MIR-548O-5P99.9471.243488
HSA-MIR-548W99.9471.243488
HSA-MIR-548Y99.9471.283514
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-314399.9371.963104
HSA-MIR-129-5P99.8870.263273
HSA-MIR-612499.8769.783551

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map DepMap (CRISPR cell-line fitness): dependent in 45.1% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 40)

  • Prevalence of SDHB, SDHC, and SDHD germline mutations in clinic patients with head and neck paragangliomas (PMID:11897817)
  • Participation of the iron-sulfur protein subunit of SDHB in development of susceptibility to familial pheochromocytoma is reconfirmed by a familial case with a germline mutation. (PMID:12362046)
  • Review. Succinate dehydrogenase catalyses a step in the Krebs tricarboxylic-acid cycle. Inherited heterozygous mutations in the gene encoding this enzyme causes a predisposition to inherited neoplasia syndromes. (PMID:12612654)
  • SDHB has a major role in the pathogenesis of familial phaeochromocytomas, but the possible role of SDHB in sporadic tumours showing allelic loss at 1p36 has yet to be ascertained. (PMID:12618761)
  • protein expression of the iron-sulfur subunit responds to the cellular iron level, thereby influencing mitochondrial respiratory function and cellular growth. (PMID:14512425)
  • Germline SDHB mutations can predispose to early-onset kidney cancers in addition to paragangliomas (PMID:14685938)
  • In patients with pheochromocytoma or functional paraganglioma with an SDHB mutation, the tumors were larger, more frequently extra-adrenal, and malignant. (PMID:16314641)
  • A possible role for SDH polymorphism as susceptibility/disease modifying factors in familial and sporadic medullary thyroid carcinomas was shown. (PMID:16322339)
  • Germline mutations of SDHB play a minor role in sporadic head and neck paraganglioma. (PMID:16405730)
  • In patients with pheochromocytoma or functional paraganglioma with an SDHB mutation, the tumors were larger, more frequently extra-adrenal, and malignant. (PMID:16472267)
  • Missense, nonsense, frameshift, and splice site mutations of the SDHB gene are associated with about half of all malignancies originating from extraadrenal paragangliomas. (PMID:16912137)
  • Familial paraganglioma syndrome type 4 caused by a mutation in the succinate dehydrogenase complex, subunit B gene. (PMID:17143317)
  • Mutations of the gene encoding succinate dehydrogenase subunit B predispose to malignant paraganglioma, but clinical expression of these tumors cannot be predicted by the genotype. (PMID:17200167)
  • SDHB mutations are associated with malignant phaeochromocytoma. Patients who present with a family history of paraganglioma or phaeochromocytoma, with multiple tumours, or early onset tumours (<50 years), should be referred for genetic investigation. (PMID:17298303)
  • Two novel SDH mutations in Japanese pheochromocytomas. (PMID:17308434)
  • SDHB mutations are associated with a high rate of malignant head and neck paragangliomas. (PMID:17599579)
  • SDHB mutations, frequent in patients with malignant pheochromocytomas or paragangliomas, are associated with shorter survival (PMID:17652212)
  • investigated 11 patients with the dyad of ‘paraganglioma and gastric stromal sarcoma’; in eight, from 7 unrelated families, the GISTs were caused by germline mutations of the genes encoding subunits B, C, or D (the SDHB, SDHC and SDHD genes, respectively) (PMID:17667967)
  • familial gastrointestinal stromal tumors may be caused by mutations of the succinate dehydrogenase subunit genes SDHB, SDHC, and SDHD (PMID:17804857)
  • Molecular genetic analysis with sequencing of the succinate dehydrogenase type B (SDHB) gene revealed a unknown mutation of codon 214 (CAG–>TAG) leading to an amino acid change of glutamine to a stop-Codon (Q214X-mutation) in exon 6 in pheochromocytoma. (PMID:17943698)
  • differences in reactive oxygen species production, HIF proliferation, and cell proliferation contribute to the differences in tumor phenotype in cells lacking SdhB as opposed to those lacking SdhA (PMID:17967865)
  • After haplotyping the SDHB region, we concluded that the deletion detected in Iberian Peninsular paraganglioma patients is probably due to a founder effect. (PMID:18057081)
  • Mutation of succinate dehydrogenase enzyme subunit B gene is associated with metastatic pheochromocytoma and paraganglioma (PMID:18310297)
  • There is a pathogenic role of the succinate dehydrogenase B mutation (R46Q) in malignant paraganglioma. (PMID:18362451)
  • An excess of SDHB mutations in paragangliomas versus pheochromocytomas was found, with no difference in the frequency of mutations in malignant versus benign paragangliomas. (PMID:18382370)
  • SDH-B mutation carriers develop disease early and predominantly in extra-adrenal locations. (PMID:18419787)
  • transient silencing of the HIF-1 alpha transcription factor in SDHB-silenced cells had little effect on expression of a subset of up-regulated genes, it partially reversed adhesion phenotype to fibronectin, indicating a role for HIF-1 in this process (PMID:18519664)
  • In this Belgian series there is a high frequency of SDHB mutations associated with head and neck paragangliomas without evidence of recurrence or malignancy. (PMID:18551016)
  • analysis of germline mutations and variants in the succinate dehydrogenase genes SDHB and SDHD in Cowden and Cowden-like syndromes (PMID:18678321)
  • Germline mutations of the SDHB gene may be associated with genetic susceptibility to renal cell carcinoma. Thus, inherited mutations in SDHB may predispose individuals to RCC. (PMID:18728283)
  • mediastinal paragangliomas are strongly associated with SDHB gene mutations (PMID:19075037)
  • Malignant paraganglioma associated with SDHB is reported in an 8-year-old child. When should genetic screening start? (PMID:19189136)
  • SDHB mutations are associated with extra-adrenal paragangliomas. (PMID:19208735)
  • we report the case of a novel SDHB mutation (L157X) in a Japanese patient with abdominal paraganglioma following malignant lung metastasis. In addition, we identified an asymptomatic carrier of the SDHB mutation in this family. (PMID:19261994)
  • A novel deletion of exon 3 of the SDHB gene was identified in nine apparently unrelated Dutch patients (PMID:19368708)
  • Variable expressivity of the phenotype associated with a large exon 1 SDHB deletion, including low penetrance, diverse primary paraganglioma tumor locations, and malignant potential (PMID:19389109)
  • Fifteen cases of PGL carried a germline mutation in SDHB or SDHD, four of which not described before. (PMID:19393419)
  • Multiple genetic alterations including mutations, polymorphisms and intronic variants are more frequently observed in malignant pheochromocytomas. (PMID:19399650)
  • no clear association was found between gene variants involved in oxygen sensing and chemoresponsiveness, although some mutations in the SDHB and SDHD genes deserve further investigations in a larger population. (PMID:19768395)
  • We report tumor risks in 358 patients with SDHB (n=295) and SDHD (n=63) mutations for head and neck paragangliomas (HNPGL), adrenal pheochromocytoma and renal tumors. (PMID:19802898)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_reriosi:dkey-31b16.7ENSDARG00000092713
mus_musculusSdhbENSMUSG00000009863
rattus_norvegicusSdhbENSRNOG00000007967
drosophila_melanogasterSdhBFBGN0014028
drosophila_melanogasterSdhBLFBGN0030975
caenorhabditis_elegansWBGENE00006433
caenorhabditis_elegansWBGENE00009626

Protein

Protein identifiers

Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrialP21912 (reviewed: P21912)

Alternative names: Iron-sulfur subunit of complex II, Malate dehydrogenase [quinone] iron-sulfur subunit

All UniProt accessions (13): A0A087WWT1, A0A087WXX8, A0AAQ5BH73, A0AAQ5BH80, A0AAQ5BH88, A0AAQ5BHA5, A0AAQ5BHB4, A0AAQ5BHC2, A0AAQ5BHC5, A0AAQ5BHC9, A0AAQ5BHD9, A0AAQ5BHE6, P21912

UniProt curated annotations — full annotation on UniProt →

Function. Iron-sulfur protein (IP) subunit of the succinate dehydrogenase complex (mitochondrial respiratory chain complex II), responsible for transferring electrons from succinate to ubiquinone (coenzyme Q). SDH also oxidizes malate to the non-canonical enol form of oxaloacetate, enol-oxaloacetate. Enol-oxaloacetate, which is a potent inhibitor of the succinate dehydrogenase activity, is further isomerized into keto-oxaloacetate.

Subunit / interactions. Component of complex II composed of four subunits: the flavoprotein (FP) SDHA, iron-sulfur protein (IP) SDHB, and a cytochrome b560 composed of SDHC and SDHD. Interacts with SDHAF1; the interaction is required for iron-sulfur cluster incorporation into SDHB. (Microbial infection) Interacts with JC virus small t antigen.

Subcellular location. Mitochondrion inner membrane.

Disease relevance. Pheochromocytoma/paraganglioma syndrome 4 (PPGL4) [MIM:115310] A form of pheochromocytoma/paraganglioma syndrome, a tumor predisposition syndrome characterized by the development of neuroendocrine tumors, usually in adulthood. Pheochromocytomas are catecholamine-producing tumors that arise from chromaffin cells in the adrenal medulla. Paragangliomas develop from sympathetic paraganglia in the thorax, abdomen, and pelvis, as well as from parasympathetic paraganglia in the head and neck. PPGL4 inheritance is autosomal dominant. The disease is caused by variants affecting the gene represented in this entry. Paraganglioma and gastric stromal sarcoma (PGGSS) [MIM:606864] Gastrointestinal stromal tumors may be sporadic or inherited in an autosomal dominant manner, alone or as a component of a syndrome associated with other tumors, such as in the context of neurofibromatosis type 1 (NF1). Patients have both gastrointestinal stromal tumors and paragangliomas. Susceptibility to the tumors was inherited in an apparently autosomal dominant manner, with incomplete penetrance. The disease is caused by variants affecting the gene represented in this entry. Mitochondrial complex II deficiency, nuclear type 4 (MC2DN4) [MIM:619224] A form of mitochondrial complex II deficiency, a disorder with heterogeneous clinical manifestations. Some patients have multisystem involvement of the brain, heart, muscle, liver, and kidneys resulting in death in infancy, whereas others have only isolated cardiac or muscle involvement with onset in adulthood and normal cognition. Clinical features include psychomotor regression in infants, poor growth with lack of speech development, severe spastic quadriplegia, dystonia, progressive leukoencephalopathy, muscle weakness, exercise intolerance, cardiomyopathy. Some patients manifest Leigh syndrome or Kearns-Sayre syndrome. MC2DN4 is a severe, autosomal recessive form characterized by early-onset progressive neurodegeneration with leukoencephalopathy. The disease is caused by variants affecting the gene represented in this entry.

Activity regulation. Enol-oxaloacetate inhibits the succinate dehydrogenase activity.

Cofactor. Binds 1 [2Fe-2S] cluster. Binds 1 [3Fe-4S] cluster. Binds 1 [4Fe-4S] cluster.

Pathway. Carbohydrate metabolism; tricarboxylic acid cycle; fumarate from succinate (eukaryal route): step 1/1.

Similarity. Belongs to the succinate dehydrogenase/fumarate reductase iron-sulfur protein family.

RefSeq proteins (2): NP_001394290, NP_002991* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR0010412Fe-2S_ferredoxin-typeDomain
IPR004489Succ_DH/fum_Rdtase_Fe-SFamily
IPR0060582Fe2S_fd_BSBinding_site
IPR009051Helical_ferredxnHomologous_superfamily
IPR012675Beta-grasp_dom_sfHomologous_superfamily
IPR0178964Fe4S_Fe-S-bdDomain
IPR0179004Fe4S_Fe_S_CSConserved_site
IPR025192Succ_DH/fum_Rdtase_NDomain
IPR0360102Fe-2S_ferredoxin-like_sfHomologous_superfamily
IPR050573SDH/FRD_Iron-SulfurFamily

Pfam: PF13085, PF13534

Enzyme classification (BRENDA):

  • EC 1.3.5.1 — succinate dehydrogenase (BRENDA: 80 organisms, 226 substrates, 192 inhibitors, 145 Km, 115 kcat entries)

Substrate kinetics (BRENDA)

28 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
SUCCINATE0.0015–2039
UBIQUINONE0.0005–0.226
FUMARATE0.005–0.45514
2,3-DIMETHOXY-5-METHYL-6-DECYL-1,4-BENZOQUINONE0.0034–0.0189
REDUCED PLUMBAGIN0.11–0.199
UBIQUINONE-20.0002–0.01149
MENAQUINOL0.0009–0.00548
PHENAZINE METHOSULFATE0.11–0.483
UBIQUINONE-10.0016–0.023
2,6-DICHLOROPHENOL INDOPHENOL0.003–0.0072
CALDARIELLAQUINONE0.06–0.182
MENAQUINONE0.0018–0.0042
OXIDIZED 2,6-DICHLOROPHENOLINDOPHENOL0.0654–0.0892
2,3-DIMETHOXY-5-METHYL-1,4-BENZOQUINONE0.0031
2,3-DIMETHYL-1,4-NAPHTHOHYDROQUINONE0.121

Catalyzed reactions (Rhea), 3 shown:

  • a quinone + succinate = fumarate + a quinol (RHEA:40523)
  • (R)-malate + a quinone = enol-oxaloacetate + a quinol (RHEA:79827)
  • (S)-malate + a quinone = enol-oxaloacetate + a quinol (RHEA:79831)

UniProt features (76 total): sequence variant 26, binding site 12, strand 10, helix 10, turn 6, sequence conflict 5, modified residue 2, domain 2, transit peptide 1, chain 1, region of interest 1

Structure

Experimental structures (PDB)

6 structures.

PDBMethodResolution (Å)
9KC4ELECTRON MICROSCOPY2.65
8GS8ELECTRON MICROSCOPY2.86
7KLVELECTRON MICROSCOPY3.1
7KCLELECTRON MICROSCOPY3.14
7KCMELECTRON MICROSCOPY3.43
7KLUELECTRON MICROSCOPY3.5

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P21912-F192.140.86

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (12): 189; 192; 196; 201; 243; 249; 253; 93; 98; 101; 113; 186

Post-translational modifications (2): 51, 55

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-611105Respiratory electron transport
R-HSA-71403Citric acid cycle (TCA cycle)
R-HSA-9854311Maturation of TCA enzymes and regulation of TCA cycle
R-HSA-1428517Aerobic respiration and respiratory electron transport
R-HSA-1430728Metabolism

MSigDB gene sets: 643 (showing top): BORCZUK_MALIGNANT_MESOTHELIOMA_UP, MODULE_151, GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_THE_CH_CH_GROUP_OF_DONORS, MORF_HDAC1, MORF_UBE2N, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, CREBP1_Q2, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, TGACCTY_ERR1_Q2, MORF_HDAC2, GOBP_NUCLEOSIDE_PHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_DICARBOXYLIC_ACID_METABOLIC_PROCESS, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS

GO Biological Process (6): tricarboxylic acid cycle (GO:0006099), succinate metabolic process (GO:0006105), mitochondrial electron transport, succinate to ubiquinone (GO:0006121), aerobic respiration (GO:0009060), respiratory electron transport chain (GO:0022904), proton motive force-driven mitochondrial ATP synthesis (GO:0042776)

GO Molecular Function (10): succinate dehydrogenase (quinone) activity (GO:0008177), electron transfer activity (GO:0009055), metal ion binding (GO:0046872), ubiquinone binding (GO:0048039), 2 iron, 2 sulfur cluster binding (GO:0051537), 3 iron, 4 sulfur cluster binding (GO:0051538), 4 iron, 4 sulfur cluster binding (GO:0051539), protein binding (GO:0005515), oxidoreductase activity (GO:0016491), iron-sulfur cluster binding (GO:0051536)

GO Cellular Component (8): nucleoplasm (GO:0005654), mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), mitochondrial matrix (GO:0005759), plasma membrane (GO:0005886), mitochondrial membrane (GO:0031966), respiratory chain complex II (succinate dehydrogenase) (GO:0045273), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Aerobic respiration and respiratory electron transport2
Citric acid cycle (TCA cycle)1
Metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
mitochondrion3
iron-sulfur cluster binding3
cellular respiration2
cellular anatomical structure2
aerobic respiration1
primary metabolic process1
dicarboxylic acid metabolic process1
aerobic electron transport chain1
mitochondrial ATP synthesis coupled electron transport1
electron transport chain1
oxidative phosphorylation1
proton motive force-driven ATP synthesis1
succinate dehydrogenase activity1
oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor1
molecular_function1
cation binding1
quinone binding1
binding1
catalytic activity1
metal cluster binding1
nuclear lumen1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
intracellular organelle lumen1
membrane1
cell periphery1
mitochondrial envelope1
organelle membrane1
membrane protein complex1
respiratory chain complex1
oxidoreductase complex1

Protein interactions and networks

STRING

5057 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SDHBSDHAP31040999
SDHBSDHCQ99643999
SDHBSDHDO14521999
SDHBSDHAF2Q9NX18998
SDHBF5H5T6F5H5T6994
SDHBUQCRC2P22695977
SDHBSDHAF1A6NFY7959
SDHBNDUFB8O95169953
SDHBTMEM127O75204935
SDHBFHP07954893
SDHBRETP07949884
SDHBMT-CO1P00395877
SDHBMT-CYBP00156847
SDHBNF1P21359823
SDHBATP5F1AP25705811

IntAct

153 interactions, top by confidence:

ABTypeScore
HSCBSDHBpsi-mi:“MI:0407”(direct interaction)0.820
SDHBSDHApsi-mi:“MI:0914”(association)0.820
HSCBSDHBpsi-mi:“MI:0915”(physical association)0.820
HSCBSDHBpsi-mi:“MI:0914”(association)0.820
SDHASDHBpsi-mi:“MI:0914”(association)0.820
SDHASDHBpsi-mi:“MI:0915”(physical association)0.820
SDHBSDHApsi-mi:“MI:0915”(physical association)0.820
SDHAF1SDHBpsi-mi:“MI:0914”(association)0.790
SDHAF1SDHBpsi-mi:“MI:0915”(physical association)0.790
SDHAF1SDHBpsi-mi:“MI:0407”(direct interaction)0.790
SDHBSDHAF1psi-mi:“MI:0914”(association)0.790
SDHBSDHAF1psi-mi:“MI:0915”(physical association)0.790

BioGRID (261): SDHB (Affinity Capture-MS), AGL (Co-fractionation), ATP6AP2 (Co-fractionation), CISD1 (Co-fractionation), COX4I1 (Co-fractionation), DLAT (Co-fractionation), GPD2 (Co-fractionation), GPI (Co-fractionation), ILVBL (Co-fractionation), MRPL45 (Co-fractionation), COX2 (Co-fractionation), NDUFA12 (Co-fractionation), NDUFA2 (Co-fractionation), NDUFA6 (Co-fractionation), NDUFB9 (Co-fractionation)

ESM2 similar proteins: A5PL98, A8WPF0, A9NNH7, B0BM36, O06914, O42772, O44074, P07014, P08066, P0AC47, P0AC48, P0AC49, P0AC50, P17596, P20921, P21801, P21911, P21912, P21913, P21914, P32420, P44893, P51053, P80480, P9WN88, P9WN89, Q007T0, Q09545, Q1RGP3, Q3B8J8, Q3T189, Q4UN71, Q54I90, Q55CC2, Q59662, Q68XS0, Q6FWS8, Q6H4G3, Q70KF8, Q75CI4

Diamond homologs: A5PL98, A8WPF0, B0BM36, D9PUX5, O42772, O44074, P07014, P0AC47, P0AC48, P0AC49, P0AC50, P17596, P20921, P21801, P21911, P21912, P21913, P21914, P32420, P48932, P48933, P51053, P80477, P80480, P9WN88, P9WN89, Q007T0, Q09545, Q1RGP3, Q3B8J8, Q3T189, Q4UN71, Q55CC2, Q57557, Q59662, Q68XS0, Q6FWS8, Q6H4G3, Q6LYC4, Q70KF8

SIGNOR signaling

4 interactions.

AEffectBMechanism
SDHAF2up-regulatesSDHBbinding
SDHB“form complex”“Succinate dehydrogenase-Mitochondrial respiratory chain complex II”binding
“iron-sulfur cluster”“up-regulates activity”SDHB“chemical activation”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 109 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Maturation of TCA enzymes and regulation of TCA cycle750.0×3e-08
Citric acid cycle (TCA cycle)526.4×2e-04
Mitochondrial protein import714.7×1e-04
Mitochondrial protein degradation710.0×9e-04
PIP3 activates AKT signaling86.7×3e-03

GO biological processes:

GO termPartnersFoldFDR
iron-sulfur cluster assembly531.0×2e-04
cellular response to epidermal growth factor stimulus516.4×3e-03
epidermal growth factor receptor signaling pathway615.3×8e-04
phosphatidylinositol 3-kinase/protein kinase B signal transduction715.2×2e-04
positive regulation of miRNA transcription515.0×3e-03
protein import into nucleus68.9×7e-03
cell population proliferation77.4×6e-03
positive regulation of ERK1 and ERK2 cascade87.0×3e-03

Disease & clinical

Cancer significance

Clinical variants and AI predictions

ClinVar

1581 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic189
Likely pathogenic65
Uncertain significance685
Likely benign340
Benign48

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1065988NM_003000.3(SDHB):c.200+1G>CPathogenic
1066588NM_003000.3(SDHB):c.557G>A (p.Cys186Tyr)Pathogenic
1069440NM_003000.3(SDHB):c.412del (p.Asp138fs)Pathogenic
1070347NM_003000.3(SDHB):c.466del (p.Tyr156fs)Pathogenic
1072823NC_000001.10:g.(?17345376)(17345463_?)delPathogenic
1072824NC_000001.10:g.(?17345376)(17371403_?)delPathogenic
1074491NM_003000.3(SDHB):c.17_18insACTCTCCTTGAGGCGCCGGTTGC (p.Ala15fs)Pathogenic
1176539GRCh37/hg19 1p36.13(chr1:17345376-17345453)x1Pathogenic
12778NM_003000.3(SDHB):c.268C>T (p.Arg90Ter)Pathogenic
12782NM_003000.3(SDHB):c.716_719del (p.Ser239fs)Pathogenic
12783NM_003000.3(SDHB):c.79C>T (p.Arg27Ter)Pathogenic
12784NM_003000.3(SDHB):c.(-151_-1)_(72+1_73-1)delPathogenic
12785NM_003000.3(SDHB):c.136C>G (p.Arg46Gly)Pathogenic
12790NM_003000.3(SDHB):c.423+1G>CPathogenic
1285202NM_003000.3(SDHB):c.200+1G>APathogenic
1326294NM_003000.3(SDHB):c.423+1G>TPathogenic
1362479NC_000001.10:g.(?17345376)(17359650_?)delPathogenic
1363102NM_003000.3(SDHB):c.598del (p.Trp200fs)Pathogenic
1371694NM_003000.3(SDHB):c.445_446dup (p.Gln149fs)Pathogenic
1380234NM_003000.3(SDHB):c.183T>A (p.Tyr61Ter)Pathogenic
1381081NM_003000.3(SDHB):c.19_41dup (p.Pro14_Ala15insSerProTer)Pathogenic
1400077NM_003000.3(SDHB):c.484G>T (p.Glu162Ter)Pathogenic
140773NM_003000.3(SDHB):c.286+2T>APathogenic
142653NM_003000.3(SDHB):c.607_616del (p.Gly203fs)Pathogenic
142763NM_003000.3(SDHB):c.136C>T (p.Arg46Ter)Pathogenic
1443907NM_003000.3(SDHB):c.450C>G (p.Tyr150Ter)Pathogenic
1452759NM_003000.3(SDHB):c.743_765+36delPathogenic
1455650NC_000001.10:g.(?17349093)(17380514_?)delPathogenic
1455849NM_003000.3(SDHB):c.243_246dup (p.Val83Ter)Pathogenic
1456331NM_003000.3(SDHB):c.75del (p.Ser26fs)Pathogenic

SpliceAI

1255 predictions. Top by Δscore:

VariantEffectΔscore
1:17018958:CCT:Cacceptor_gain1.0000
1:17018960:T:Cacceptor_gain1.0000
1:17022603:CGTA:Cdonor_loss1.0000
1:17022604:GTA:Gdonor_loss1.0000
1:17022605:TAC:Tdonor_loss1.0000
1:17022606:ACC:Adonor_loss1.0000
1:17022607:C:CTdonor_loss1.0000
1:17022726:TAGGC:Tacceptor_gain1.0000
1:17022728:GGCC:Gacceptor_loss1.0000
1:17022729:GCCTG:Gacceptor_loss1.0000
1:17022730:CCTGG:Cacceptor_loss1.0000
1:17022731:C:CCacceptor_gain1.0000
1:17022731:CTGG:Cacceptor_loss1.0000
1:17022732:T:Aacceptor_loss1.0000
1:17027758:A:ACdonor_gain1.0000
1:17027759:C:CCdonor_gain1.0000
1:17027759:CG:Cdonor_gain1.0000
1:17027759:CGCT:Cdonor_gain1.0000
1:17027795:T:Adonor_gain1.0000
1:17028598:A:ACdonor_gain1.0000
1:17028599:C:CCdonor_gain1.0000
1:17033143:CAT:Cacceptor_gain1.0000
1:17044753:ATACT:Adonor_loss1.0000
1:17044757:TCA:Tdonor_loss1.0000
1:17044758:CACTT:Cdonor_loss1.0000
1:17044759:A:ACdonor_gain1.0000
1:17044760:C:CAdonor_gain1.0000
1:17044760:CT:Cdonor_gain1.0000
1:17044760:CTT:Cdonor_gain1.0000
1:17044760:CTTA:Cdonor_gain1.0000

AlphaMissense

1835 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:17022646:A:GC243R1.000
1:17024029:A:GC196R1.000
1:17024059:A:GC186R1.000
1:17022614:A:CC253W0.999
1:17022615:C:TC253Y0.999
1:17022616:A:GC253R0.999
1:17022626:G:CC249W0.999
1:17022627:C:TC249Y0.999
1:17022628:A:GC249R0.999
1:17022644:G:CC243W0.999
1:17022645:C:AC243F0.999
1:17022645:C:GC243S0.999
1:17022645:C:TC243Y0.999
1:17022646:A:TC243S0.999
1:17022704:T:AR223S0.999
1:17022704:T:GR223S0.999
1:17022705:C:AR223I0.999
1:17022705:C:GR223T0.999
1:17022721:A:GW218R0.999
1:17022721:A:TW218R0.999
1:17022723:C:GR217P0.999
1:17022724:G:TR217S0.999
1:17023992:C:TG208E0.999
1:17023993:C:GG208R0.999
1:17023993:C:TG208R0.999
1:17024021:G:CS198R0.999
1:17024021:G:TS198R0.999
1:17024023:T:GS198R0.999
1:17024027:G:CC196W0.999
1:17024028:C:TC196Y0.999

dbSNP variants (sampled 300 via entrez): RS1000040715 (1:17035471 C>T), RS1000158338 (1:17047868 T>C,G), RS1000341001 (1:17030102 T>G), RS1000501757 (1:17036787 C>A,T), RS1000507925 (1:17018668 A>C,G), RS1000582771 (1:17024680 G>A), RS1000694609 (1:17042818 C>T), RS1000760553 (1:17049557 A>G), RS1000786527 (1:17031260 G>C), RS1000965442 (1:17049301 CTTTT>C,CTTT,CTTTTT,CTTTTTT), RS1001036889 (1:17055138 G>A), RS1001173587 (1:17023622 C>T), RS1001191146 (1:17049829 T>C,G), RS1001293246 (1:17048749 C>A,G,T), RS1001314422 (1:17054248 C>A,G,T)

Disease associations

OMIM: gene MIM:185470 | disease phenotypes: MIM:115310, MIM:171300, MIM:606764, MIM:168000, MIM:193300, MIM:606864, MIM:619224, MIM:158350, MIM:604287, MIM:167000, MIM:252011

GenCC curated gene-disease

DiseaseClassificationInheritance
pheochromocytoma/paraganglioma syndrome 4DefinitiveAutosomal dominant
hereditary pheochromocytoma-paragangliomaDefinitiveAutosomal dominant
gastrointestinal stromal tumorDefinitiveAutosomal dominant
Carney-Stratakis syndromeDefinitiveAutosomal dominant
pheochromocytomaDefinitiveAutosomal dominant
renal cell carcinomaStrongAutosomal dominant
mitochondrial complex 2 deficiency, nuclear type 4StrongAutosomal recessive
Cowden diseaseSupportiveAutosomal dominant
mitochondrial complex II deficiencySupportiveAutosomal recessive

ClinGen Gene-Disease Validity (2)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
mitochondrial diseaseDefinitiveAR
hereditary pheochromocytoma-paragangliomaDefinitiveAD

Mondo (19): pheochromocytoma/paraganglioma syndrome 4 (MONDO:0007273), pheochromocytoma (MONDO:0008233), gastrointestinal stromal tumor (MONDO:0011719), hereditary neoplastic syndrome (MONDO:0015356), hereditary pheochromocytoma-paraganglioma (MONDO:0017366), von Hippel-Lindau disease (MONDO:0008667), Carney-Stratakis syndrome (MONDO:0011740), mitochondrial complex 2 deficiency, nuclear type 4 (MONDO:0030974), Cowden disease (MONDO:0016063), breast cancer (MONDO:0007254), paraganglioma (MONDO:0000448), renal cell carcinoma (MONDO:0005086), Carney triad (MONDO:0011424), Cowden syndrome 1 (MONDO:0008021), ovarian cancer (MONDO:0008170)

Orphanet (11): Inherited cancer-predisposing syndrome (Orphanet:140162), Hereditary pheochromocytoma-paraganglioma (Orphanet:29072), Gastrointestinal stromal tumor (Orphanet:44890), Von Hippel-Lindau disease (Orphanet:892), Carney-Stratakis syndrome (Orphanet:97286), Cowden syndrome (Orphanet:201), Renal cell carcinoma (Orphanet:217071), Carney triad (Orphanet:139411), Rare ovarian cancer (Orphanet:213500), Hereditary papillary renal cell carcinoma (Orphanet:47044), Isolated succinate-CoQ reductase deficiency (Orphanet:3208)

HPO phenotypes

214 total (30 of 214 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000007Autosomal recessive inheritance
HP:0000036Abnormal penis morphology
HP:0000076Vesicoureteral reflux
HP:0000077Abnormality of the kidney
HP:0000093Proteinuria
HP:0000096Glomerular sclerosis
HP:0000130Abnormality of the uterus
HP:0000158Macroglossia
HP:0000218High palate
HP:0000221Furrowed tongue
HP:0000252Microcephaly
HP:0000256Macrocephaly
HP:0000360Tinnitus
HP:0000365Hearing impairment
HP:0000405Conductive hearing impairment
HP:0000478Abnormality of the eye
HP:0000518Cataract
HP:0000526Aniridia
HP:0000544External ophthalmoplegia
HP:0000545Myopia
HP:0000580Pigmentary retinopathy
HP:0000618Blindness
HP:0000639Nystagmus
HP:0000717Autism
HP:0000726Dementia
HP:0000737Irritability
HP:0000740Episodic paroxysmal anxiety
HP:0000750Delayed speech and language development
HP:0000767Pectus excavatum

GWAS associations

24 associations (top):

StudyTraitp-value
GCST000611_7Height2.000000e-07
GCST010696_16Cortical thickness (min-P)8.000000e-11
GCST010697_21Cortical surface area (min-P)1.000000e-08
GCST010698_46Subcortical volume (min-P)2.000000e-11
GCST010699_5Brain morphology (min-P)7.000000e-11
GCST010700_46Cortical thickness (MOSTest)2.000000e-10
GCST010701_63Cortical surface area (MOSTest)3.000000e-14
GCST010702_161Subcortical volume (MOSTest)2.000000e-20
GCST010703_70Brain morphology (MOSTest)2.000000e-08
GCST012226_410Waist circumference adjusted for body mass index2.000000e-08
GCST012226_411Waist circumference adjusted for body mass index4.000000e-14
GCST012226_412Waist circumference adjusted for body mass index1.000000e-08
GCST012226_413Waist circumference adjusted for body mass index1.000000e-12
GCST012227_1377Hip circumference adjusted for BMI1.000000e-12
GCST012227_1379Hip circumference adjusted for BMI4.000000e-14
GCST012227_1380Hip circumference adjusted for BMI2.000000e-15
GCST90020024_4A body shape index2.000000e-11
GCST90020024_5A body shape index5.000000e-10
GCST90020024_6A body shape index5.000000e-12
GCST90020028_565Hip circumference adjusted for BMI2.000000e-09
GCST90020028_660Hip circumference adjusted for BMI1.000000e-14
GCST90020028_664Hip circumference adjusted for BMI2.000000e-08
GCST90020029_1249Waist circumference adjusted for body mass index1.000000e-13
GCST90020029_1250Waist circumference adjusted for body mass index2.000000e-10

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0004346neuroimaging measurement
EFO:0004840cortical thickness
EFO:0007789BMI-adjusted waist circumference
EFO:0008039BMI-adjusted hip circumference

MeSH disease descriptors (11)

DescriptorNameTree numbers
D002292Carcinoma, Renal CellC04.557.470.200.025.390; C04.588.945.947.535.160; C12.050.351.937.820.535.160; C12.050.351.968.419.473.160; C12.200.758.820.750.160; C12.200.777.419.473.160; C12.900.820.535.160; C12.950.419.473.160; C12.950.983.535.160
D046152Gastrointestinal Stromal TumorsC04.557.450.565.370; C06.301.371.308; C06.405.249.308
D006223Hamartoma Syndrome, MultipleC04.445.435; C04.651.435; C04.700.435; C16.320.700.435
D009386Neoplastic Syndromes, HereditaryC04.700; C16.320.700
D010051Ovarian NeoplasmsC04.588.322.455; C12.050.351.500.056.630.705; C12.050.351.937.418.685; C12.100.250.056.630.705; C12.900.418.685; C19.344.410; C19.391.630.705
D010235ParagangliomaC04.557.465.625.650.700; C04.557.580.625.650.700
D010673PheochromocytomaC04.557.465.625.650.700.725; C04.557.580.625.650.700.725
D006623von Hippel-Lindau DiseaseC10.562.925; C14.907.077.925; C16.131.077.245.750; C16.320.184.750
C565803Carney Triad (supp.)
C564650Carney-Stratakis Syndrome (supp.)
C565375Mitochondrial Complex II Deficiency (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4105824 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

Binding affinities (BindingDB)

4 measured of 4 human assays (4 total across all organisms); most potent 4 below. Values come from heterogeneous assays and are not directly comparable.

LigandMeasureValuePatent
N-(1-adamantyl)-4-[4-[1-[(3,4-dimethoxyphenyl)methyl]-6-oxo-3-pyridinyl]-6-(trifluoromethyl)pyrimidin-2-yl]sulfonylbutanamideEC50500 nMUS-11725000: Apoptosis inhibitors
N-(1-adamantyl)-4-[4-(difluoromethyl)-6-[1-[(3,4-dimethoxyphenyl)methyl]-6-oxo-3-pyridinyl]pyrimidin-2-yl]sulfonylbutanamideEC50500 nMUS-11725000: Apoptosis inhibitors
N-(1-adamantyl)-4-[4-[1-(1,3-benzodioxol-5-ylmethyl)-5-fluoro-6-oxo-3-pyridinyl]-6-methylpyrimidin-2-yl]sulfonylbutanamideEC50500 nMUS-11725000: Apoptosis inhibitors
N-(1-adamantyl)-4-[4-[5-fluoro-1-[(3-methylbenzotriazol-5-yl)methyl]-6-oxo-3-pyridinyl]-6-methylpyrimidin-2-yl]sulfonylbutanamideEC50500 nMUS-11725000: Apoptosis inhibitors

ChEMBL bioactivities

36 potent at pChembl≥5 of 39 total, top 36 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
9.64EC500.23nMCHEMBL4078870
9.38EC500.42nMCHEMBL4078870
8.85EC501.4nMCHEMBL4078220
7.60EC5025nMCHEMBL4091379
7.57EC5027nMCHEMBL4064603
7.24EC5057nMCHEMBL4070501
7.18EC5066nMCHEMBL4061878
7.16EC5069nMCHEMBL4092330
7.03EC5094nMCHEMBL4082074
6.96EC50110nMCHEMBL4071549
6.79EC50164nMCHEMBL4086114
6.67EC50216nMCHEMBL4093871
6.60EC50253nMCHEMBL4083596
6.59EC50257nMCHEMBL4089942
6.55EC50282nMCHEMBL4073188
6.44EC50364nMCHEMBL4101603
6.13EC50749nMCHEMBL1430895
6.09EC50817nMCHEMBL4101046
5.95EC501135nMCHEMBL4070722
5.94EC501143nMCHEMBL4063455
5.94EC501157nMCHEMBL4085084
5.84EC501428nMCHEMBL4097841
5.80EC501591nMCHEMBL4090123
5.74EC501821nMCHEMBL4097672
5.66EC502201nMCHEMBL1492648
5.46EC503489nMCHEMBL4063532
5.46EC503487nMCHEMBL4096202
5.45EC503516nMCHEMBL4086039
5.40EC504000nMCHEMBL4103147
5.39EC504060nMCHEMBL4074296
5.38EC504207nMCHEMBL4062092
5.35EC504477nMCHEMBL4100077
5.20EC506355nMCHEMBL4078150
5.18EC506642nMCHEMBL4104624
5.15EC507033nMCHEMBL4103961
5.06EC508756nMCHEMBL4088482

PubChem BioAssay actives

36 with measured affinity, of 60 total; 35 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
N-(1-adamantyl)-4-[4-[1-[(3,4-dimethoxyphenyl)methyl]-6-oxo-3-pyridinyl]-6-(trifluoromethyl)pyrimidin-2-yl]sulfonylbutanamide1427665: Inhibition of SDHB in human U2OS cells over-expressing tBid assessed as reduction in apoptosis preincubated for 1 hr followed by doxycyclin addition to induce tBid protein expression measured after 24 hrs by Cell Titer-Glo assayec500.0002uM
1-[(3,4-dimethoxyphenyl)methyl]-5-[2-(4-oxo-4-piperidin-1-ylbutyl)sulfonyl-6-(trifluoromethyl)pyrimidin-4-yl]pyridin-2-one1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec500.0014uM
1-[(3,4-dimethoxyphenyl)methyl]-5-[2-methylsulfonyl-6-(trifluoromethyl)pyrimidin-4-yl]pyridin-2-one1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec500.0250uM
1-[(3,4-dimethoxyphenyl)methyl]-5-[2-(4-oxo-4-pyrrolidin-1-ylbutyl)sulfonyl-6-(trifluoromethyl)pyrimidin-4-yl]pyridin-2-one1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec500.0270uM
1-[(3-methoxyphenyl)methyl]-5-[2-methylsulfonyl-6-(trifluoromethyl)pyrimidin-4-yl]pyridin-2-one1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec500.0570uM
1-[(4-chlorophenyl)methyl]-5-[2-methylsulfonyl-6-(trifluoromethyl)pyrimidin-4-yl]pyridin-2-one1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec500.0660uM
5-[2-methylsulfonyl-6-(trifluoromethyl)pyrimidin-4-yl]-1-[(3-propoxyphenyl)methyl]pyridin-2-one1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec500.0690uM
1-[(4-methoxyphenyl)methyl]-5-[2-methylsulfonyl-6-(trifluoromethyl)pyrimidin-4-yl]pyridin-2-one1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec500.0940uM
1-[(3-ethoxyphenyl)methyl]-5-[2-methylsulfonyl-6-(trifluoromethyl)pyrimidin-4-yl]pyridin-2-one1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec500.1100uM
4-[4-[1-[(3,4-dimethoxyphenyl)methyl]-6-oxo-3-pyridinyl]-6-(trifluoromethyl)pyrimidin-2-yl]sulfonyl-N,N-dimethylbutanamide1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec500.1640uM
1-[(3,4-dimethoxyphenyl)methyl]-5-[2-(2-methoxyethylsulfonyl)-6-(trifluoromethyl)pyrimidin-4-yl]pyridin-2-one1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec500.2160uM
1-[(3,4-dimethoxyphenyl)methyl]-5-[2-heptylsulfonyl-6-(trifluoromethyl)pyrimidin-4-yl]pyridin-2-one1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec500.2530uM
1-[(3-chlorophenyl)methyl]-5-[2-methylsulfonyl-6-(trifluoromethyl)pyrimidin-4-yl]pyridin-2-one1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec500.2570uM
1-[(3,4-dimethoxyphenyl)methyl]-5-[2-(3-methoxypropylsulfonyl)-6-(trifluoromethyl)pyrimidin-4-yl]pyridin-2-one1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec500.2820uM
1-[(3,4-dimethoxyphenyl)methyl]-5-[2-pentylsulfonyl-6-(trifluoromethyl)pyrimidin-4-yl]pyridin-2-one1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec500.3640uM
2-methylsulfonyl-4-thiophen-2-yl-6-(trifluoromethyl)pyrimidine1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec500.7490uM
1-[(4-ethynylphenyl)methyl]-5-[2-methylsulfonyl-6-(trifluoromethyl)pyrimidin-4-yl]pyridin-2-one1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec500.8170uM
ethyl 3-[4-thiophen-2-yl-6-(trifluoromethyl)pyrimidin-2-yl]sulfonylpropanoate1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec501.1350uM
1-[(2-chlorophenyl)methyl]-5-[2-methylsulfonyl-6-(trifluoromethyl)pyrimidin-4-yl]pyridin-2-one1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec501.1430uM
1-benzyl-5-[2-methylsulfonyl-6-(trifluoromethyl)pyrimidin-4-yl]pyridin-2-one1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec501.1570uM
2-ethylsulfonyl-4-thiophen-2-yl-6-(trifluoromethyl)pyrimidine1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec501.4280uM
2-(2-phenylethylsulfonyl)-4-thiophen-2-yl-6-(trifluoromethyl)pyrimidine1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec501.5910uM
1-[(3-hydroxyphenyl)methyl]-5-[2-methylsulfonyl-6-(trifluoromethyl)pyrimidin-4-yl]pyridin-2-one1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec501.8210uM
2-methylsulfonyl-4-phenyl-6-(trifluoromethyl)pyrimidine1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec502.2010uM
4-(3-methylphenyl)-2-methylsulfonyl-6-(trifluoromethyl)pyrimidine1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec503.4870uM
4-[[5-[2-methylsulfonyl-6-(trifluoromethyl)pyrimidin-4-yl]-2-oxo-1-pyridinyl]methyl]benzonitrile1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec503.4890uM
methyl 3-[2-methylsulfonyl-6-(trifluoromethyl)pyrimidin-4-yl]benzoate1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec503.5160uM
N-(2-hydroxy-5-methylphenyl)-4-[4-thiophen-2-yl-6-(trifluoromethyl)pyrimidin-2-yl]sulfonylbutanamide1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec504.0000uM
3-[[5-[2-methylsulfonyl-6-(trifluoromethyl)pyrimidin-4-yl]-2-oxo-1-pyridinyl]methyl]benzonitrile1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec504.0600uM
2-[(4-phenylphenyl)methylsulfonyl]-4-thiophen-2-yl-6-(trifluoromethyl)pyrimidine1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec504.2070uM
1-[(3-ethynylphenyl)methyl]-5-[2-methylsulfonyl-6-(trifluoromethyl)pyrimidin-4-yl]pyridin-2-one1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec504.4770uM
4-(4-methylphenyl)-2-methylsulfonyl-6-(trifluoromethyl)pyrimidine1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec506.3550uM
4-(2-methylphenyl)-2-methylsulfonyl-6-(trifluoromethyl)pyrimidine1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec506.6420uM
methyl 2-[2-methylsulfonyl-6-(trifluoromethyl)pyrimidin-4-yl]benzoate1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec507.0330uM
2-methylsulfonyl-4-(3-phenoxyphenyl)-6-(trifluoromethyl)pyrimidine1427662: Inhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayec508.7560uM

CTD chemical–gene interactions

71 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aincreases abundance, affects cotreatment, increases methylation, decreases expression, increases expression (+1 more)5
Acetaminophenaffects cotreatment, decreases expression2
Aerosolsdecreases expression2
Benzo(a)pyreneaffects methylation, decreases expression2
1-Methyl-4-phenylpyridiniumdecreases expression, increases reaction2
Particulate Matterdecreases expression, increases abundance, increases expression, affects cotreatment2
bisphenol Fincreases expression1
ginger extractdecreases reaction, increases abundance, increases expression1
lasiocarpinedecreases expression1
triphenyl phosphateaffects expression1
alpha-pineneincreases abundance, affects cotreatment, decreases expression1
lead acetatedecreases reaction, increases abundance, decreases expression1
pyrogallol 1,3-dimethyl etherincreases expression, affects cotreatment1
plastochromanol 8decreases expression1
2,6-dichloro-4-nitrophenoldecreases expression1
sodium arseniteincreases expression1
2-bromopalmitateincreases abundance, increases palmitoylation, decreases reaction1
nickel chlorideincreases expression1
perfluorooctanoic aciddecreases expression1
ochratoxin Adecreases expression1
methacrylaldehydeincreases abundance, affects cotreatment, decreases expression1
isobutyl alcoholaffects cotreatment, decreases expression, increases abundance1
S-1,2-dichlorovinyl-N-acetylcysteineaffects expression1
demethoxycurcumindecreases expression1
di-n-butylphosphoric acidaffects expression1
azoxystrobinincreases expression1
chloropicrinincreases expression1
pyrimidifenincreases expression1
bisphenol Bincreases expression1
olaparibincreases response to substance1

ChEMBL screening assays

4 unique, capped per target: 4 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL3994501BindingInhibition of SDHB in human U2OS cells over-expressing Bim assessed as inhibition of apoptosis preincubated for 1 hr followed by doxycyclin addition to induce Bim protein expression measured after 24 hrs by Cell Titer-Glo assayDiscovery of Highly Potent 2-Sulfonyl-Pyrimidinyl Derivatives for Apoptosis Inhibition and Ischemia Treatment. — ACS Med Chem Lett

Cellosaurus cell lines

5 cell lines: 3 cancer cell line, 1 transformed cell line, 1 telomerase immortalized cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B0YFAbcam HEK293 SDHB KOTransformed cell lineFemale
CVCL_C6JRhPheo1 KD-SDHBTelomerase immortalized cell lineFemale
CVCL_D1UBAbcam U-87MG SDHB KOCancer cell lineMale
CVCL_D7ZZUbigene A-549 SDHB KOCancer cell lineMale
CVCL_E0N8Ubigene HeLa SDHB KOCancer cell lineFemale

Clinical trials (associated diseases)

595 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00414765PHASE4COMPLETEDAldesleukin in Participants With Metastatic Renal Cell Carcinoma or Metastatic Melanoma
NCT00777504PHASE4UNKNOWNStudy to the Optimal Duration of Therapy With Oral Angiogenesis Inhibitors
NCT00930345PHASE4TERMINATEDBiological, Pathological and Imagery Markers in the First-line Treatment of Metastatic Clear-cell Renal Cell Carcinoma
NCT01206764PHASE4COMPLETEDA Trial of Everolimis in Patients With Advanced Renal Cell Carcinoma.
NCT01266837PHASE4COMPLETEDOpen Label, Single Arm Trial to Characterize Patients With Metastatic RCC Treated With Everolimus After Failure of the First VEGF-targeted Therapy (MARC-2)
NCT02056587PHASE4COMPLETEDEverolimus in Patients With Metastatic Renal Cell Carcinoma Following Progression on Prior Bevacizumab Treatment
NCT02338570PHASE4TERMINATEDOutcome-related Factors in Patients With Metastatic Renal Cell Carcinoma Treated With Everolimus (ORCHIDEE)
NCT02596035PHASE4COMPLETEDAn Investigational Immuno-therapy Safety Trial of Nivolumab in Patients With Advanced or Metastatic Renal Cell Carcinoma
NCT02982954PHASE4COMPLETEDA Study to Evaluate the Safety of Nivolumab and Ipilimumab in Subjects With Previously Untreated Advanced or Metastatic Renal Cell Cancer
NCT05949424PHASE4UNKNOWNOPTI - DOSE: Optimal Dosing of Oral Anticancer Drugs in Older Adults
NCT07028125PHASE4RECRUITINGDigital Monitoring of Self-reported Symptoms by Patients Treated With Cabozantinib Plus Nivolumab for Advanced Clear-cell Renal Carcinoma
NCT07405086PHASE4RECRUITINGMorning Versus Afternoon Administration of Immunotherapy for the Treatment of Advanced or Metastatic Solid Tumors, The Knight SHIFT Study
NCT01379898PHASE4COMPLETEDPhenoxybenzamine Versus Doxazosin in PCC Patients
NCT01959711PHASE4COMPLETEDRandomized Clinical Trial of Posterior Retroperitoneoscopic Adrenalectomy Versus Lateral Laparoscopic Adrenalectomy
NCT05702944PHASE4RECRUITINGThe Effect and Safety of Omitting Preoperative Alpha-adrenergic Blockade for Normotensive Pheochromocytoma
NCT00171977PHASE4COMPLETEDPost-Marketing Clinical Study of Postoperative Adjuvant Therapy With Imatinib Mesylate in Patients With Gastrointestinal Stromal Tumors (GIST)
NCT00510354PHASE4COMPLETEDTreatment of Patients With Everolimus and Imatinib Mesylate Who Have Progressive Gastro Intestinal Stromal Tumors (GIST) and Are Resistant to Imatinib Mesylate
NCT00756509PHASE4COMPLETEDTreatment of Patients With Metastatic or Unresectable Gastrointestinal Stromal Tumors in First Line With Nilotinib
NCT02800330PHASE4COMPLETEDThe Effects of the Proton Pump Inhibitor Esomeprazole on the Bioavailability of Regorafenib
NCT04825574PHASE4COMPLETEDStudy for Patients Previously Treated in Avapritinib Clinical Trials
NCT00033904PHASE3COMPLETEDSurvival Study Of Oncophage® vs. Observation In Patients With Kidney Cancer
NCT00126178PHASE3TERMINATEDClinical Trial Studying a Personalized Cancer Vaccine in Patients With Non-metastatic Kidney Cancer
NCT00291369PHASE3COMPLETEDCytokines in Patients With Metastatic Renal Cell Carcinoma of Intermediate Prognosis
NCT00410124PHASE3COMPLETEDRAD001 Plus Best Supportive Care (BSC) Versus BSC Plus Placebo in Patients With Metastatic Carcinoma of the Kidney Which Has Progressed After Treatment With Sorafenib and/or Sunitinib
NCT00474786PHASE3COMPLETEDTemsirolimus Versus Sorafenib As Second-Line Therapy In Patients With Advanced RCC Who Have Failed First-Line Sunitinib
NCT00478114PHASE3COMPLETEDEfficacy and Safety of Sorafenib in Advanced Renal Cell Carcinoma (RCC)
NCT00606632PHASE3COMPLETEDPre-surgical Detection of Clear Cell Renal Cell Carcinoma (ccRCC) Using Radiolabeled G250-Antibody
NCT00606866PHASE3COMPLETEDMRI Study of BAY 43-9006 in Metastatic Renal Cell Carcinoma
NCT00631371PHASE3COMPLETEDStudy Comparing Bevacizumab + Temsirolimus vs. Bevacizumab + Interferon-Alfa In Advanced Renal Cell Carcinoma Subjects
NCT00732914PHASE3COMPLETEDSequential Study to Treat Renal Cell Carcinoma
NCT00869011PHASE3UNKNOWNExercise for Patients With Renal Cell Cancer Receiving Sunitinib
NCT00930033PHASE3COMPLETEDClinical Trial to Assess the Importance of Nephrectomy
NCT01030783PHASE3COMPLETEDA Study to Compare Tivozanib (AV-951) to Sorafenib in Subjects With Advanced Renal Cell Carcinoma
NCT01076010PHASE3COMPLETEDAn Extension Treatment Protocol for Subjects Who Have Participated in a Study of Tivozanib Versus Sorafenib in Kidney Carcinoma (Protocol AV-951-09-301).
NCT01198158PHASE3TERMINATEDEverolimus With or Without Bevacizumab in Treating Patients With Advanced Kidney Cancer That Progressed After First-Line Therapy
NCT01223027PHASE3COMPLETEDStudy of Dovitinib Versus Sorafenib in Patients With Metastatic Renal Cell Carcinoma
NCT01224288PHASE3ACTIVE_NOT_RECRUITINGDynamic Contrast Enhancement Computed Tomography for Evaluating Tumor Perfusion in Patients With Metastatic Renal Cell Carcinoma Receiving Targeted Therapies: Renal Cell Carcinoma (RCC) Scramble
NCT01235962PHASE3COMPLETEDA Study to Evaluate Pazopanib as an Adjuvant Treatment for Localized Renal Cell Carcinoma (RCC)
NCT01265810PHASE3COMPLETEDCaphosol in Oral Mucositis Due to Targeted Therapy
NCT01265901PHASE3COMPLETEDIMA901 in Patients Receiving Sunitinib for Advanced/Metastatic Renal Cell Carcinoma