CA13

gene
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Also known as CAXIIIFLJ37995MGC59868

Summary

CA13 (carbonic anhydrase 13, HGNC:14914) is a protein-coding gene on chromosome 8q21.2, encoding Carbonic anhydrase 13 (Q8N1Q1). Reversible hydration of carbon dioxide.

Predicted to enable carbonate dehydratase activity. Predicted to be located in intracellular membrane-bounded organelle and myelin sheath. Predicted to be active in cytosol.

Source: NCBI Gene 377677 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 49 total
  • Druggable target: yes — 26 molecules with ChEMBL bioactivity
  • MANE Select transcript: NM_198584

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14914
Approved symbolCA13
Namecarbonic anhydrase 13
Location8q21.2
Locus typegene with protein product
StatusApproved
AliasesCAXIII, FLJ37995, MGC59868
Ensembl geneENSG00000185015
Ensembl biotypeprotein_coding
OMIM611436
Entrez377677

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding_CDS_not_defined, 1 protein_coding, 1 retained_intron

ENST00000321764, ENST00000517298, ENST00000517831, ENST00000518392, ENST00000522631

RefSeq mRNA: 1 — MANE Select: NM_198584 NM_198584

CCDS: CCDS6236

Canonical transcript exons

ENST00000321764 — 7 exons

ExonStartEnd
ENSE000012628168528123085284073
ENSE000012628268524545885245865
ENSE000034760118526847285268627
ENSE000034925048525074085250937
ENSE000035891838525942185259539
ENSE000035935448526790285267964
ENSE000036562128526660885266703

Expression profiles

Bgee: expression breadth ubiquitous, 239 present calls, max score 97.56.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.3835 / max 142.4954, expressed in 1544 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
896072.6258892
896102.1496912
896030.9763532
896060.7154372
896050.4442166
896080.2907101
896040.110150
896090.071642

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
jejunal mucosaUBERON:000039997.56gold quality
palpebral conjunctivaUBERON:000181296.83gold quality
epithelial cell of pancreasCL:000008395.38gold quality
ileal mucosaUBERON:000033195.14gold quality
esophagus squamous epitheliumUBERON:000692091.58gold quality
nasal cavity epitheliumUBERON:000538490.38gold quality
amniotic fluidUBERON:000017390.22gold quality
endothelial cellCL:000011590.14gold quality
gingival epitheliumUBERON:000194990.09gold quality
upper arm skinUBERON:000426389.82gold quality
duodenumUBERON:000211489.61gold quality
upper leg skinUBERON:000426287.96gold quality
oral cavityUBERON:000016787.46gold quality
gingivaUBERON:000182887.28gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099185.21gold quality
pancreatic ductal cellCL:000207984.74gold quality
parietal pleuraUBERON:000240084.14gold quality
germinal epithelium of ovaryUBERON:000130483.66gold quality
epithelium of nasopharynxUBERON:000195183.26gold quality
oocyteCL:000002383.18gold quality
nasal cavity mucosaUBERON:000182681.98gold quality
visceral pleuraUBERON:000240181.85gold quality
secondary oocyteCL:000065581.15gold quality
lower esophagus mucosaUBERON:003583481.11gold quality
pylorusUBERON:000116680.68gold quality
pharyngeal mucosaUBERON:000035580.10gold quality
small intestineUBERON:000210879.57gold quality
mucosa of transverse colonUBERON:000499179.57gold quality
parotid glandUBERON:000183179.26gold quality
skin of hipUBERON:000155479.25gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes6.24

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

118 targeting CA13, 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-4262100.0073.263931
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-6740-5P100.0065.64932
HSA-MIR-8485100.0077.574731
HSA-MIR-126-5P100.0072.713180
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-428299.9975.366408
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-607799.9968.042299
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-1213699.9872.815713
HSA-MIR-56899.9869.862084
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-651-3P99.9473.485177
HSA-MIR-314399.9371.963104
HSA-MIR-4760-3P99.9370.502385
HSA-MIR-218-5P99.9372.222103
HSA-MIR-7-1-3P99.9171.534384

Literature-anchored findings (GeneRIF, showing 5)

  • a unique and widespread distribution pattern for CA XIII compared with the other cytosolic CA isozymes. May play important physiological roles in several organs (PMID:14600151)
  • cytosolic CA I, II, and XIII are downregulated in neoplastic colorectal mucosa compared to normal colorectal mucosa (PMID:15836783)
  • Cytosolic carbonic anhydrase XIII may have a role in maintaining the acid-base balance in the kidney and the gastrointestinal and reproductive tracts. [review] (PMID:18336313)
  • investigation of residues modulating the catalytic features of one of the least investigated cytosolic isoform, hCA XIII; results showed that residues assisting the formation of an ordered solvent network within the catalytic site as well as those forming a histidine cluster on the protein surface are important to guarantee an efficient proton transfer (PMID:31431090)
  • Carbonic anhydrase 13 suppresses bone metastasis in breast cancer. (PMID:33588197)

Cross-species orthologs

18 orthologs

OrganismSymbolGene ID
danio_reriocahzENSDARG00000011166
danio_rerioca2ENSDARG00000014488
mus_musculusCar13ENSMUSG00000027555
rattus_norvegicusCar13ENSRNOG00000021323
drosophila_melanogasterCAH13FBGN0033542
drosophila_melanogasterCAH14FBGN0034554
drosophila_melanogasterCAH15FBGN0034560
drosophila_melanogasterCAH7FBGN0037788
drosophila_melanogasterCAH8FBGN0038956
drosophila_melanogasterCAH4FBGN0039235
drosophila_melanogasterCAH9FBGN0039486
drosophila_melanogasterCAH6FBGN0039838
drosophila_melanogasterCAH16FBGN0040628
drosophila_melanogasterCAH5FBGN0040629
drosophila_melanogasterCARPBFBGN0052698
caenorhabditis_elegansWBGENE00000279
caenorhabditis_elegansWBGENE00000283
caenorhabditis_eleganscah-6WBGENE00000284

Paralogs (14): CA11 (ENSG00000063180), CA12 (ENSG00000074410), CA2 (ENSG00000104267), CA9 (ENSG00000107159), CA14 (ENSG00000118298), CA6 (ENSG00000131686), CA1 (ENSG00000133742), CA10 (ENSG00000154975), CA3 (ENSG00000164879), CA4 (ENSG00000167434), CA7 (ENSG00000168748), CA5B (ENSG00000169239), CA5A (ENSG00000174990), CA8 (ENSG00000178538)

Protein

Protein identifiers

Carbonic anhydrase 13Q8N1Q1 (reviewed: Q8N1Q1)

Alternative names: Carbonate dehydratase XIII, Carbonic anhydrase XIII

All UniProt accessions (1): Q8N1Q1

UniProt curated annotations — full annotation on UniProt →

Function. Reversible hydration of carbon dioxide.

Tissue specificity. Expressed in thymus, small intestine, spleen, prostate, ovary, colon and testis.

Activity regulation. Inhibited by acetazolamide.

Similarity. Belongs to the alpha-carbonic anhydrase family.

RefSeq proteins (1): NP_940986* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001148CA_domDomain
IPR018338Carbonic_anhydrase_a-class_CSConserved_site
IPR023561Carbonic_anhydrase_a-classFamily
IPR036398CA_dom_sfHomologous_superfamily

Pfam: PF00194

Catalyzed reactions (Rhea), 1 shown:

  • hydrogencarbonate + H(+) = CO2 + H2O (RHEA:10748)

UniProt features (36 total): strand 15, helix 10, binding site 4, turn 3, chain 1, domain 1, active site 1, sequence variant 1

Structure

Experimental structures (PDB)

18 structures.

PDBMethodResolution (Å)
5OGJX-RAY DIFFRACTION1.06
4KNNX-RAY DIFFRACTION1.4
5OHHX-RAY DIFFRACTION1.42
5LLAX-RAY DIFFRACTION1.5
5E2NX-RAY DIFFRACTION1.53
3D0NX-RAY DIFFRACTION1.55
4QIZX-RAY DIFFRACTION1.55
5LLNX-RAY DIFFRACTION1.6
4QJPX-RAY DIFFRACTION1.62
4QSJX-RAY DIFFRACTION1.7
6G5UX-RAY DIFFRACTION1.7
9FPVX-RAY DIFFRACTION1.7
4KNMX-RAY DIFFRACTION1.9
9FPWX-RAY DIFFRACTION1.9
4HU1X-RAY DIFFRACTION1.95
4QJXX-RAY DIFFRACTION1.95
3CZVX-RAY DIFFRACTION2
3DA2X-RAY DIFFRACTION2.05

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N1Q1-F196.740.97

Functional residue map

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

Catalytic / active sites (1): 65 (proton donor/acceptor)

Ligand- & substrate-binding residues (4): 95; 97; 120; 200–201

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-1475029Reversible hydration of carbon dioxide
R-HSA-1430728Metabolism

MSigDB gene sets: 147 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, GSE45365_NK_CELL_VS_CD8A_DC_UP, GSE45365_NK_CELL_VS_BCELL_UP, GOMF_CARBONATE_DEHYDRATASE_ACTIVITY, MARTINEZ_RB1_TARGETS_UP, MCBRYAN_PUBERTAL_BREAST_4_5WK_DN, WANG_RESPONSE_TO_BEXAROTENE_UP, AACTTT_UNKNOWN, GOMF_HYDRO_LYASE_ACTIVITY, MARTINEZ_RB1_AND_TP53_TARGETS_UP, POS_RESPONSE_TO_HISTAMINE_UP, GAUSSMANN_MLL_AF4_FUSION_TARGETS_D_UP, GEORGES_TARGETS_OF_MIR192_AND_MIR215, YATGNWAAT_OCT_C, KIM_MYCN_AMPLIFICATION_TARGETS_UP

GO Biological Process (0):

GO Molecular Function (5): carbonate dehydratase activity (GO:0004089), zinc ion binding (GO:0008270), protein binding (GO:0005515), lyase activity (GO:0016829), metal ion binding (GO:0046872)

GO Cellular Component (3): cytoplasm (GO:0005737), cytosol (GO:0005829), myelin sheath (GO:0043209)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
hydro-lyase activity1
transition metal ion binding1
binding1
catalytic activity1
cation binding1
intracellular anatomical structure1
cytoplasm1

Protein interactions and networks

STRING

937 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CA13CYP24A1Q07973848
CA13ALBP02768576
CA13TGP01266535
CA13RNASE1P07998531
CA13FTH1P02794501
CA13ATRNO75882448
CA13SLC4A4Q9Y6R1375
CA13PHF24Q9UPV7374
CA13TMEM59Q9BXS4370
CA13DGKDQ16760353
CA13UMODP07911353
CA13MAST2Q6P0Q8353
CA13STK40Q8N2I9353
CA13CABIN1Q9Y6J0353
CA13BLNKQ8WV28348

IntAct

7 interactions, top by confidence:

ABTypeScore
CA13CRACR2Bpsi-mi:“MI:0915”(physical association)0.560
CRTC3CA13psi-mi:“MI:0915”(physical association)0.560
CA13CRACR2Bpsi-mi:“MI:0915”(physical association)0.000
CA13CRTC3psi-mi:“MI:0915”(physical association)0.000

BioGRID (7): CA13 (Two-hybrid), CA13 (Two-hybrid), CA13 (Affinity Capture-RNA), CA13 (Affinity Capture-MS), CA13 (Co-fractionation), CA13 (Co-fractionation), CA13 (Protein-peptide)

ESM2 similar proteins: B0BNN3, O76206, P00441, P00445, P00915, P00916, P00917, P00918, P00919, P00920, P00921, P00922, P07450, P07451, P07452, P07630, P13634, P14141, P16015, P27139, P28755, P35217, P43166, P48282, P48284, P60052, P82205, P83299, Q0IIW3, Q1LZA1, Q27504, Q3SZX4, Q42961, Q5S1S4, Q6C662, Q7M316, Q7M317, Q8HXQ0, Q8HXQ1, Q8HXQ2

Diamond homologs: A0A7H0DN92, A0JN41, B0BNN3, O57211, P00915, P00916, P00917, P00918, P00919, P00920, P00921, P04195, P07450, P07451, P07452, P07630, P0DSY1, P0DSY2, P13634, P14141, P16015, P20508, P23470, P23471, P23589, P27139, P35217, P35218, P43165, P43166, P48282, P48283, P61215, P83299, Q05909, Q1LZA1, Q3SZX4, Q5R4U0, Q5S1S4, Q66HG6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance32
Likely benign2
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1262 predictions. Top by Δscore:

VariantEffectΔscore
8:85250722:T:TAacceptor_gain1.0000
8:85250730:T:Gacceptor_gain1.0000
8:85250731:A:AGacceptor_gain1.0000
8:85250732:T:Gacceptor_gain1.0000
8:85250733:A:AGacceptor_gain1.0000
8:85250737:A:AGacceptor_gain1.0000
8:85250737:AAGGT:Aacceptor_loss1.0000
8:85250738:A:Gacceptor_gain1.0000
8:85250739:G:GCacceptor_loss1.0000
8:85259419:A:AGacceptor_gain1.0000
8:85259420:G:GTacceptor_gain1.0000
8:85259420:GTTCT:Gacceptor_gain1.0000
8:85261281:A:AGacceptor_gain1.0000
8:85261281:ACAT:Aacceptor_gain1.0000
8:85261283:AT:Aacceptor_gain1.0000
8:85261284:T:Gacceptor_gain1.0000
8:85266594:T:Gacceptor_gain1.0000
8:85266605:CAGCT:Cacceptor_loss1.0000
8:85266606:A:AGacceptor_gain1.0000
8:85266606:AGCT:Aacceptor_loss1.0000
8:85266607:G:GCacceptor_gain1.0000
8:85266607:GCTC:Gacceptor_gain1.0000
8:85266607:GCTCC:Gacceptor_gain1.0000
8:85266700:ACAG:Adonor_loss1.0000
8:85266701:CAGGT:Cdonor_loss1.0000
8:85266702:AGGT:Adonor_loss1.0000
8:85266703:GGTG:Gdonor_loss1.0000
8:85266704:G:GCdonor_loss1.0000
8:85266705:T:Gdonor_loss1.0000
8:85267892:A:AGacceptor_gain1.0000

AlphaMissense

1722 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:85268586:T:AW210R0.986
8:85268586:T:CW210R0.986
8:85266680:G:CA143P0.983
8:85266609:T:CL119P0.982
8:85250753:G:CW17C0.981
8:85250753:G:TW17C0.981
8:85281299:C:AR247S0.981
8:85250803:T:CI34T0.980
8:85266656:G:CA135P0.980
8:85266681:C:AA143D0.980
8:85281323:C:AR255S0.980
8:85268535:T:AW193R0.978
8:85268535:T:CW193R0.978
8:85268550:T:CS198P0.977
8:85250908:T:AV69D0.976
8:85259477:T:AW98R0.976
8:85259477:T:CW98R0.976
8:85250803:T:GI34S0.975
8:85250888:C:AN62K0.975
8:85250888:C:GN62K0.975
8:85259505:A:TE107V0.974
8:85259539:G:CE118D0.974
8:85259539:G:TE118D0.974
8:85250751:T:AW17R0.973
8:85250751:T:CW17R0.973
8:85259474:C:GH97D0.973
8:85268548:G:AG197D0.973
8:85259534:G:CA117P0.972
8:85281324:G:CR255P0.972
8:85259509:C:AH108Q0.971

dbSNP variants (sampled 300 via entrez): RS1000033976 (8:85244770 A>G), RS1000041156 (8:85257293 T>G), RS1000104442 (8:85259348 G>A,T), RS1000141425 (8:85250023 C>G,T), RS1000142024 (8:85277598 T>G), RS1000149123 (8:85274714 G>C,T), RS1000203349 (8:85274538 T>C), RS1000421999 (8:85278892 CATCTGTA>C), RS1000534456 (8:85275748 A>G), RS1000629537 (8:85267811 TA>T,TAA), RS1000657932 (8:85255324 G>A), RS1000730439 (8:85256951 C>T), RS1000794197 (8:85271577 G>A,T), RS1000884345 (8:85248913 TAGA>T), RS1000903433 (8:85275861 C>T)

Disease associations

OMIM: gene MIM:611436 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

StudyTraitp-value
GCST002040_1Blood trace element (Zn levels)6.000000e-12
GCST006585_2472Blood protein levels4.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (2): CHEMBL2095180 (PROTEIN FAMILY), CHEMBL3912 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

26 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 671,587 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL19METHAZOLAMIDE465
CHEMBL20ACETAZOLAMIDE428,768
CHEMBL750ZONISAMIDE416,649
CHEMBL118CELECOXIB4112,844
CHEMBL1200471PYRITHIONE ZINC424,834
CHEMBL1286LEVETIRACETAM413,997
CHEMBL17DICHLORPHENAMIDE49,022
CHEMBL18ETHOXZOLAMIDE43,042
CHEMBL21SULFANILAMIDE4153,075
CHEMBL2105581VERALIPRIDE41,165
CHEMBL218490DORZOLAMIDE410,216
CHEMBL220491BRINZOLAMIDE48,355
CHEMBL220492TOPIRAMATE435,160
CHEMBL325041BORTEZOMIB413,120
CHEMBL406INDAPAMIDE416,097
CHEMBL58323LACOSAMIDE45,692
CHEMBL865VALDECOXIB441,681
CHEMBL902FAMOTIDINE466,828
CHEMBL926DOBUTAMINE417,095
CHEMBL140CURCUMIN393,882
CHEMBL165RESVERATROL3
CHEMBL508338THIMEROSAL3
CHEMBL251680COUMAPHOS2
CHEMBL4297315PCI-274832
CHEMBL6246ELLAGIC ACID2
CHEMBL69759SONEPIPRAZOLE2

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

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — Carbonic anhydrases

Most potent curated ligand interactions (1 total), top 1:

LigandActionAffinityParameter
acetazolamideInhibition7.77pKi

Binding affinities (BindingDB)

44 measured of 58 human assays (61 total across all organisms); most potent 44 below. Values come from heterogeneous assays and are not directly comparable.

LigandMeasureValue
2-Chloro-4-{[2-(methylthio)-1H-benzimidazol-1-yl]acetyl}-benzenesulfonamide (2j)KD1.67 nM
2-Chloro-4-[(2-propyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamide (2f)KD2.86 nM
4-[(2-Butyl-1H-benzimidazol-1-yl)acetyl]-2-chlorobenzenesulfonamide (2g)KD3.33 nM
4-{[2-(Methylsulfanyl)-1H-benzimidazol-1-yl]acetyl}benzenesulfonamide (1j)KD3.57 nM
4-[(2-Isopropyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamide (1h)KD4 nM
2-Chloro-4-[(2-ethyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamide (2e)KD4.76 nM
2-Chloro-4-[(2-isopropyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamide (2h)KD5 nM
2-Chloro-4-[(2-methyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamide (2b)KD5.88 nM
2-Chloro-4-[(2-isobutyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamide (2i)KD6.67 nM
4-[(2-Propyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamide (1f)KD7.14 nM
4-{[2-(Hydroxymethyl)-1H-benzimidazol-1-yl]acetyl}benzenesulfonamide (1c)KD8.33 nM
4-[(2-Benzyl-1H-benzimidazol-1-yl)acetyl]-2-chlorobenzenesulfonamide (2d)KD8.33 nM
4-[(2-Ethyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamide (1e)KD8.33 nM
4-[(2-Isobutyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamide (1i)KD8.33 nM
4-[(2-Methyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamide (1b)KD10 nM
2-Chloro-4-{[2-(hydroxymethyl)-1H-benzimidazol-1-yl]acetyl}benzenesulfonamide (2c)KD10 nM
4-[(2-Butyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamide (1g)KD11.1 nM
4-(1H-benzimidazol-1-ylacetyl)-2-chlorobenzenesulfonamide (2a)KD12 nM
4-(1H-benzimidazol-1-ylacetyl)benzenesulfonamide (1a)KD33 nM
3-[(2-Isobutyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamide (3i)KD125 nM
4-[(2-Benzyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamide (1d)KD143 nM
Topiramate, 3KI250 nM
3-[(2-Butyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamide (3g)KD667 nM
Investigational agent, 5KI810 nM
Investigational agent, 4KI850 nM
3-[(2-Propyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamide (3f)KD1000 nM
3-{[2-(Methylthio)-1H-benzimidazol-1-yl]acetyl}benzenesulfonamide (3j)KD1670 nM
3-[(2-Benzyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamide (3d)KD2500 nM
3-[(2-Isopropyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamide (3h)KD2500 nM
2-Chloro-5-[(2-isobutyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamideKD3330 nM
3-(1H-benzimidazol-1-ylacetyl)benzenesulfonamide (3a)KD4350 nM
2-Chloro-5-[(2-isopropyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamideKD4540 nM
3-[(2-Ethyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamide (3e)KD4760 nM
3-{[2-(Hydroxymethyl)-1H-benzimidazol-1-yl]acetyl}benzenesulfonamide (3c)KD5000 nM
2-Chloro-5-{[2-(methylsulfanyl)-1H-benzimidazol-1-yl]acetyl}benzenesulfonamideKD5000 nM
2-Chloro-5-[(2-ethyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamideKD7140 nM
2-Chloro-5-{[2-(hydroxymethyl)-1H-benzimidazol-1-yl]acetyl}benzenesulfonamideKD7140 nM
5-[(2-Benzyl-1H-benzimidazol-1-yl)acetyl]-2-chlorobenzenesulfonamideKD8330 nM
3-[(2-Methyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamide (3b)KD9090 nM
4-chloro-N-(2-methyl-2,3-dihydro-1H-indol-1-yl)-3-sulfamoylbenzamideKD10000 nM
2-Chloro-5-[(2-propyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamideKD10000 nM
5-[(2-Butyl-1H-benzimidazol-1-yl)acetyl]-2-chlorobenzenesulfonamideKD10000 nM
2-Chloro-5-[(2-methyl-1H-benzimidazol-1-yl)acetyl]benzenesulfonamideKD10000 nM
5-(1H-Benzimidazol-1-ylacetyl)-2-chlorobenzenesulfonamideKD11100 nM

ChEMBL bioactivities

749 potent at pChembl≥5 of 766 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
10.96Kd0.011nMCHEMBL4461481
10.80Kd0.016nMCHEMBL4473602
10.80Kd0.016nMCHEMBL4464359
10.72Kd0.019nMCHEMBL4539340
10.42Kd0.038nMCHEMBL4463683
10.30Kd0.05nMCHEMBL2333416
10.24Kd0.058nMCHEMBL2010994
10.24Kd0.057nMCHEMBL4441730
10.20Kd0.063nMCHEMBL4555622
10.15Kd0.07nMCHEMBL4578934
10.12Kd0.076nMCHEMBL4475315
10.05Kd0.09nMCHEMBL4466140
10.00Kd0.1nMCHEMBL4515586
9.96Kd0.11nMCHEMBL4457904
9.92Kd0.12nMCHEMBL4543024
9.89Kd0.13nMCHEMBL4456851
9.85Kd0.14nMCHEMBL4553790
9.85Kd0.14nMCHEMBL4468834
9.82Kd0.15nMCHEMBL4577993
9.82Kd0.15nMCHEMBL4586089
9.77Kd0.17nMCHEMBL2443188
9.72Kd0.19nMCHEMBL3798446
9.70Kd0.2nMCHEMBL4517728
9.70Ki0.2nMCHEMBL4552380
9.70Ki0.2nMCHEMBL4460315
9.70Ki0.2nMCHEMBL4434661
9.70Ki0.2nMCHEMBL282157
9.66Kd0.22nMCHEMBL2333406
9.66Kd0.22nMCHEMBL4555586
9.64Kd0.23nMCHEMBL4168966
9.64Kd0.23nMCHEMBL4458989
9.64Kd0.23nMCHEMBL4573916
9.64Kd0.23nMCHEMBL4451500
9.64Kd0.23nMCHEMBL4539233
9.60Kd0.25nMCHEMBL2333411
9.60Kd0.25nMCHEMBL4452277
9.60Kd0.25nMCHEMBL4569008
9.59Kd0.26nMCHEMBL4450545
9.55Kd0.28nMCHEMBL4446052
9.54Kd0.29nMCHEMBL4444784
9.54Kd0.29nMCHEMBL4456084
9.52Kd0.3nMCHEMBL4441652
9.52Kd0.3nMCHEMBL4558457
9.52Kd0.3nMCHEMBL4450456
9.52Ki0.3nMP-CHLOROBENZENESULFONAMIDE
9.48Kd0.33nMCHEMBL4160627
9.48Kd0.33nMCHEMBL4441818
9.47Kd0.34nMCHEMBL4450306
9.47Kd0.34nMCHEMBL4454599
9.40Kd0.4nMCHEMBL2333407

PubChem BioAssay actives

798 with measured affinity, of 1111 total; 50 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
1-(2-chloro-3,5-dimethyl-4-sulfamoylphenyl)-N-(3,5-dimethylpyrazol-1-yl)-5-oxopyrrolidine-3-carboxamide1515324: Binding affinity to recombinant human CA13 assessed as intrinsic dissociation constant by DSF-based fluorescence thermal shift assaykd<0.0001uM
N-[(E)-benzylideneamino]-1-(2-chloro-3,5-dimethyl-4-sulfamoylphenyl)-5-oxopyrrolidine-3-carboxamide1515324: Binding affinity to recombinant human CA13 assessed as intrinsic dissociation constant by DSF-based fluorescence thermal shift assaykd<0.0001uM
1-[[1-(2-chloro-3,5-dimethyl-4-sulfamoylphenyl)-5-oxopyrrolidine-3-carbonyl]amino]-3-phenylthiourea1515324: Binding affinity to recombinant human CA13 assessed as intrinsic dissociation constant by DSF-based fluorescence thermal shift assaykd<0.0001uM
methyl 1-(2-chloro-3,5-dimethyl-4-sulfamoylphenyl)-5-oxopyrrolidine-3-carboxylate1515324: Binding affinity to recombinant human CA13 assessed as intrinsic dissociation constant by DSF-based fluorescence thermal shift assaykd<0.0001uM
3-chloro-2,6-dimethyl-4-[2-oxo-4-(4-phenyl-5-sulfanylidene-1H-1,2,4-triazol-3-yl)pyrrolidin-1-yl]benzenesulfonamide1515324: Binding affinity to recombinant human CA13 assessed as intrinsic dissociation constant by DSF-based fluorescence thermal shift assaykd<0.0001uM
4-bromo-N-(2-hydroxyethyl)-2-(2-phenylethylsulfanyl)-5-sulfamoylbenzamide1520089: Binding affinity to recombinant human carbonic anhydrase 13 expressed in Escherichia coli expression system assessed as kinetic dissociation constant fluorescent thermal shift assaykd0.0001uM
4-bromo-N-butyl-2-(2-phenylethylsulfanyl)-5-sulfamoylbenzamide1520089: Binding affinity to recombinant human carbonic anhydrase 13 expressed in Escherichia coli expression system assessed as kinetic dissociation constant fluorescent thermal shift assaykd0.0001uM
N-butyl-4-chloro-2-(2-phenylethylsulfanyl)-5-sulfamoylbenzamide1520089: Binding affinity to recombinant human carbonic anhydrase 13 expressed in Escherichia coli expression system assessed as kinetic dissociation constant fluorescent thermal shift assaykd0.0001uM
4-[2-[(4-tert-butyl-6-oxo-1H-pyrimidin-2-yl)sulfanyl]acetyl]benzenesulfonamide1469006: Binding affinity to human N-terminal full length His-tagged CA13 (1 to 262 residues) expressed in Escherichia coli BL21(DE3) assessed as intrinsic thermodynamic equilibrium constant at pH 7 by SPR assaykd0.0001uM
1-(2-chloro-3,5-dimethyl-4-sulfamoylphenyl)-N-[(E)-(4-methoxyphenyl)methylideneamino]-5-oxopyrrolidine-3-carboxamide1515324: Binding affinity to recombinant human CA13 assessed as intrinsic dissociation constant by DSF-based fluorescence thermal shift assaykd0.0001uM
3-chloro-2,6-dimethyl-4-[2-oxo-4-(2-sulfanylidene-3H-1,3,4-oxadiazol-5-yl)pyrrolidin-1-yl]benzenesulfonamide1515324: Binding affinity to recombinant human CA13 assessed as intrinsic dissociation constant by DSF-based fluorescence thermal shift assaykd0.0001uM
4-chloro-2-(2-phenylethylsulfanyl)-5-sulfamoylbenzamide1520089: Binding affinity to recombinant human carbonic anhydrase 13 expressed in Escherichia coli expression system assessed as kinetic dissociation constant fluorescent thermal shift assaykd0.0001uM
N-[(E)-(4-bromophenyl)methylideneamino]-1-(2-chloro-3,5-dimethyl-4-sulfamoylphenyl)-5-oxopyrrolidine-3-carboxamide1515324: Binding affinity to recombinant human CA13 assessed as intrinsic dissociation constant by DSF-based fluorescence thermal shift assaykd0.0001uM
4-chloro-2-cyclohexylsulfanyl-5-sulfamoylbenzoic acid1520089: Binding affinity to recombinant human carbonic anhydrase 13 expressed in Escherichia coli expression system assessed as kinetic dissociation constant fluorescent thermal shift assaykd0.0001uM
1-(2-bromophenyl)-5-oxo-N-(4-sulfamoylphenyl)pyrrolidine-3-carboxamide1515324: Binding affinity to recombinant human CA13 assessed as intrinsic dissociation constant by DSF-based fluorescence thermal shift assaykd0.0001uM
1-(2-chloro-3,5-dimethyl-4-sulfamoylphenyl)-N-[(E)-(4-nitrophenyl)methylideneamino]-5-oxopyrrolidine-3-carboxamide1515324: Binding affinity to recombinant human CA13 assessed as intrinsic dissociation constant by DSF-based fluorescence thermal shift assaykd0.0001uM
1-[[1-(3,5-dimethyl-4-sulfamoylphenyl)-5-oxopyrrolidine-3-carbonyl]amino]-3-phenylthiourea1515324: Binding affinity to recombinant human CA13 assessed as intrinsic dissociation constant by DSF-based fluorescence thermal shift assaykd0.0001uM
4-chloro-2-(2-phenylethylsulfanyl)-5-sulfamoylbenzoic acid1520089: Binding affinity to recombinant human carbonic anhydrase 13 expressed in Escherichia coli expression system assessed as kinetic dissociation constant fluorescent thermal shift assaykd0.0001uM
4-chloro-2-cyclohexylsulfanyl-5-sulfamoylbenzamide1520089: Binding affinity to recombinant human carbonic anhydrase 13 expressed in Escherichia coli expression system assessed as kinetic dissociation constant fluorescent thermal shift assaykd0.0001uM
2,3,5,6-tetrafluoro-4-(2-hydroxyethylsulfanyl)benzenesulfonamide1469006: Binding affinity to human N-terminal full length His-tagged CA13 (1 to 262 residues) expressed in Escherichia coli BL21(DE3) assessed as intrinsic thermodynamic equilibrium constant at pH 7 by SPR assaykd0.0001uM
4-bromo-2-cyclohexylsulfanyl-N-(2-hydroxyethyl)-5-sulfamoylbenzamide1520089: Binding affinity to recombinant human carbonic anhydrase 13 expressed in Escherichia coli expression system assessed as kinetic dissociation constant fluorescent thermal shift assaykd0.0002uM
2-(benzylamino)-4-chloro-N-(2-hydroxyethyl)-5-sulfamoylbenzamide1361391: Binding affinity to recombinant human carbonic anhydrase 13 (1 to 262 residues) expressed in Escherichia coli Rosetta 2 (DE3) strain assessed as intrinsic Kd in presence of ANS by fluorescent thermal shift assaykd0.0002uM
N-butyl-4-chloro-2-cyclohexylsulfanyl-5-sulfamoylbenzamide1520089: Binding affinity to recombinant human carbonic anhydrase 13 expressed in Escherichia coli expression system assessed as kinetic dissociation constant fluorescent thermal shift assaykd0.0002uM
4-[2-(benzimidazol-1-yl)acetyl]-2-chlorobenzenesulfonamide1469006: Binding affinity to human N-terminal full length His-tagged CA13 (1 to 262 residues) expressed in Escherichia coli BL21(DE3) assessed as intrinsic thermodynamic equilibrium constant at pH 7 by SPR assaykd0.0002uM
4-[1-[(2R)-1-(3-azabicyclo[3.2.2]nonan-3-yl)-3-methyl-1-oxobutan-2-yl]triazol-4-yl]benzenesulfonamide1557414: Inhibition of carbonic anhydrase (unknown origin)ki0.0002uM
3-chloro-4-[4-(hydrazinecarbonyl)-2-oxopyrrolidin-1-yl]-2,6-dimethylbenzenesulfonamide1515324: Binding affinity to recombinant human CA13 assessed as intrinsic dissociation constant by DSF-based fluorescence thermal shift assaykd0.0002uM
4-(2-chloro-3,5-dimethyl-4-sulfamoylanilino)-3-(4-phenyl-5-sulfanylidene-1H-1,2,4-triazol-3-yl)butanoic acid1515324: Binding affinity to recombinant human CA13 assessed as intrinsic dissociation constant by DSF-based fluorescence thermal shift assaykd0.0002uM
(2R)-3-phenyl-2-[4-(4-sulfamoylphenyl)triazol-1-yl]-N-(2-thiophen-3-ylethyl)propanamide1557414: Inhibition of carbonic anhydrase (unknown origin)ki0.0002uM
1-(2,5-dimethyl-4-sulfamoylphenyl)-N-[(E)-(4-nitrophenyl)methylideneamino]-5-oxopyrrolidine-3-carboxamide1515324: Binding affinity to recombinant human CA13 assessed as intrinsic dissociation constant by DSF-based fluorescence thermal shift assaykd0.0002uM
1-(2-chloro-3,5-dimethyl-4-sulfamoylphenyl)-N-[(E)-(4-chlorophenyl)methylideneamino]-5-oxopyrrolidine-3-carboxamide1515324: Binding affinity to recombinant human CA13 assessed as intrinsic dissociation constant by DSF-based fluorescence thermal shift assaykd0.0002uM
4-nitrobenzenesulfonamide50173: Compound was evaluated for the inhibition of Carbonic anhydraseki0.0002uM
(2R)-N-benzyl-3-methyl-2-[4-(4-sulfamoylphenyl)triazol-1-yl]butanamide1557414: Inhibition of carbonic anhydrase (unknown origin)ki0.0002uM
2,3,5,6-tetrafluoro-4-(2-phenylethylsulfanyl)benzenesulfonamide732709: Binding affinity to human recombinant CA13 at 37 degC and pH 7.0 by thermal shift assaykd0.0002uM
2-chloro-4-(2-pyrimidin-2-ylsulfanylacetyl)benzenesulfonamide1469006: Binding affinity to human N-terminal full length His-tagged CA13 (1 to 262 residues) expressed in Escherichia coli BL21(DE3) assessed as intrinsic thermodynamic equilibrium constant at pH 7 by SPR assaykd0.0002uM
4-bromo-N-butyl-2-cyclohexylsulfanyl-5-sulfamoylbenzamide1520089: Binding affinity to recombinant human carbonic anhydrase 13 expressed in Escherichia coli expression system assessed as kinetic dissociation constant fluorescent thermal shift assaykd0.0003uM
N-butyl-4-chloro-2-cyclohexylsulfonyl-5-sulfamoylbenzamide1520089: Binding affinity to recombinant human carbonic anhydrase 13 expressed in Escherichia coli expression system assessed as kinetic dissociation constant fluorescent thermal shift assaykd0.0003uM
4-chloro-2-cyclohexylsulfanyl-N-(2-hydroxyethyl)-5-sulfamoylbenzamide1520089: Binding affinity to recombinant human carbonic anhydrase 13 expressed in Escherichia coli expression system assessed as kinetic dissociation constant fluorescent thermal shift assaykd0.0003uM
4-chloro-2-cyclohexylsulfanyl-N-(2-methoxyethyl)-5-sulfamoylbenzamide1520089: Binding affinity to recombinant human carbonic anhydrase 13 expressed in Escherichia coli expression system assessed as kinetic dissociation constant fluorescent thermal shift assaykd0.0003uM
4-bromo-N-butyl-2-cyclohexylsulfonyl-5-sulfamoylbenzamide1520089: Binding affinity to recombinant human carbonic anhydrase 13 expressed in Escherichia coli expression system assessed as kinetic dissociation constant fluorescent thermal shift assaykd0.0003uM
4-chloro-2-(cyclooctylamino)-5-sulfamoylbenzoic acid1361391: Binding affinity to recombinant human carbonic anhydrase 13 (1 to 262 residues) expressed in Escherichia coli Rosetta 2 (DE3) strain assessed as intrinsic Kd in presence of ANS by fluorescent thermal shift assaykd0.0003uM
methyl 1-(3,5-dimethyl-4-sulfamoylphenyl)-5-oxopyrrolidine-3-carboxylate1515324: Binding affinity to recombinant human CA13 assessed as intrinsic dissociation constant by DSF-based fluorescence thermal shift assaykd0.0003uM
4-chloro-2-(2-phenylethylsulfonyl)-5-sulfamoylbenzamide1520089: Binding affinity to recombinant human carbonic anhydrase 13 expressed in Escherichia coli expression system assessed as kinetic dissociation constant fluorescent thermal shift assaykd0.0003uM
N-[(E)-benzylideneamino]-1-(2,5-dimethyl-4-sulfamoylphenyl)-5-oxopyrrolidine-3-carboxamide1515324: Binding affinity to recombinant human CA13 assessed as intrinsic dissociation constant by DSF-based fluorescence thermal shift assaykd0.0003uM
1-(2-chloro-3,5-dimethyl-4-sulfamoylphenyl)-5-oxopyrrolidine-3-carboxylic acid1515324: Binding affinity to recombinant human CA13 assessed as intrinsic dissociation constant by DSF-based fluorescence thermal shift assaykd0.0003uM
2-benzylsulfanyl-4-chloro-5-sulfamoylbenzamide1520089: Binding affinity to recombinant human carbonic anhydrase 13 expressed in Escherichia coli expression system assessed as kinetic dissociation constant fluorescent thermal shift assaykd0.0003uM
4-chloro-2-phenylsulfanyl-5-sulfamoylbenzamide1520089: Binding affinity to recombinant human carbonic anhydrase 13 expressed in Escherichia coli expression system assessed as kinetic dissociation constant fluorescent thermal shift assaykd0.0003uM
2,6-dimethyl-4-[2-oxo-4-(4-phenyl-5-sulfanylidene-1H-1,2,4-triazol-3-yl)pyrrolidin-1-yl]benzenesulfonamide1515324: Binding affinity to recombinant human CA13 assessed as intrinsic dissociation constant by DSF-based fluorescence thermal shift assaykd0.0003uM
4-chlorobenzenesulfonamide50173: Compound was evaluated for the inhibition of Carbonic anhydraseki0.0003uM
4-(1,3-benzothiazol-2-ylsulfanyl)-2,3,5,6-tetrafluorobenzenesulfonamide732709: Binding affinity to human recombinant CA13 at 37 degC and pH 7.0 by thermal shift assaykd0.0003uM
2-benzylsulfanyl-N-butyl-4-chloro-5-sulfamoylbenzamide1520089: Binding affinity to recombinant human carbonic anhydrase 13 expressed in Escherichia coli expression system assessed as kinetic dissociation constant fluorescent thermal shift assaykd0.0004uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression8
Cyclosporineincreases expression4
entinostataffects cotreatment, increases expression2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Tobacco Smoke Pollutionaffects expression, decreases expression2
p-Chloromercuribenzoic Acidaffects cotreatment, increases expression2
GSK-J4decreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
bisphenol Adecreases methylation1
oryzalinaffects binding, decreases activity1
trichostatin Aincreases expression1
butyraldehydeincreases expression1
nickel sulfatedecreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
mercuric bromideaffects cotreatment, increases expression1
pentanalincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
2,2’,4,4’,5-brominated diphenyl etherincreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, increases expression1
jinfukangaffects cotreatment, decreases expression1
Panobinostataffects cotreatment, increases expression1
Acetazolamideaffects binding, decreases activity1
Arsenicaffects methylation1
Benzo(a)pyrenedecreases methylation, increases methylation1
Cisplatinaffects cotreatment, decreases expression1
Doxorubicindecreases expression1
Folic Aciddecreases expression1
Golddecreases expression1

ChEMBL screening assays

96 unique, capped per target: 93 binding, 3 admet

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL3386760BindingInhibition of carbonic anhydrase (unknown origin)Substituted thieno[2,3-b]thiophenes and related congeners: Synthesis, β-glucuronidase inhibition activity, crystal structure, and POM analyses. — Bioorg Med Chem
CHEMBL4187341ADMETBinding affinity to recombinant human full length N-terminal His-tagged carbonic anhydrase 13 (1 to 262 residues) expressed in Escherichia coli BL21 (DE3) in presence of ANS by fluorescent thermal shift assayBenzimidazole design, synthesis, and docking to build selective carbonic anhydrase VA inhibitors. — Bioorg Med Chem

Clinical trials (associated diseases)

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