MTHFD2

Summary

MTHFD2 (methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase, HGNC:7434) is a protein-coding gene on chromosome 2p13.1, encoding Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial (P13995). Although its dehydrogenase activity is NAD-specific, it can also utilize NADP at a reduced efficiency.

This gene encodes a nuclear-encoded mitochondrial bifunctional enzyme with methylenetetrahydrofolate dehydrogenase and methenyltetrahydrofolate cyclohydrolase activities. The enzyme functions as a homodimer and is unique in its absolute requirement for magnesium and inorganic phosphate. Formation of the enzyme-magnesium complex allows binding of NAD. Alternative splicing results in two different transcripts, one protein-coding and the other not protein-coding. This gene has a pseudogene on chromosome 7.

Source: NCBI Gene 10797 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 67 total
• Druggable target: yes
• MANE Select transcript: NM_006636

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:7434
Approved symbol	MTHFD2
Name	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase
Location	2p13.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000065911
Ensembl biotype	protein_coding
OMIM	604887
Entrez	10797

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 13 protein_coding, 4 nonsense_mediated_decay, 3 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000394053, ENST00000409601, ENST00000409804, ENST00000462026, ENST00000470592, ENST00000477455, ENST00000488086, ENST00000489041, ENST00000677170, ENST00000677299, ENST00000677377, ENST00000677558, ENST00000677997, ENST00000678228, ENST00000678340, ENST00000678623, ENST00000678633, ENST00000678684, ENST00000678731, ENST00000678955, ENST00000679055

RefSeq mRNA: 2 — MANE Select: NM_006636 NM_001410192, NM_006636

CCDS: CCDS1935

Canonical transcript exons

ENST00000394053 — 8 exons

Exon	Start	End
ENSE00001908688	74214079	74217565
ENSE00003496681	74211199	74211291
ENSE00003538742	74211741	74211866
ENSE00003596874	74207704	74207826
ENSE00003601079	74209942	74210049
ENSE00003636870	74208569	74208721
ENSE00003657216	74205705	74205889
ENSE00003685472	74198615	74198742

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 98.95.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 109.5619 / max 1168.1303, expressed in 1825 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
21012	109.4553	1825
21013	0.1066	48

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cartilage tissue	UBERON:0002418	98.95	gold quality
descending thoracic aorta	UBERON:0002345	98.09	gold quality
blood vessel layer	UBERON:0004797	97.77	gold quality
endometrium epithelium	UBERON:0004811	97.77	gold quality
popliteal artery	UBERON:0002250	97.70	gold quality
tibial artery	UBERON:0007610	97.69	gold quality
aorta	UBERON:0000947	97.49	gold quality
thoracic aorta	UBERON:0001515	97.30	gold quality
ascending aorta	UBERON:0001496	97.21	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	97.19	gold quality
left coronary artery	UBERON:0001626	97.19	gold quality
coronary artery	UBERON:0001621	96.77	gold quality
right coronary artery	UBERON:0001625	96.75	gold quality
stromal cell of endometrium	CL:0002255	96.51	gold quality
tibia	UBERON:0000979	96.20	gold quality
vermiform appendix	UBERON:0001154	96.06	gold quality
islet of Langerhans	UBERON:0000006	96.05	gold quality
calcaneal tendon	UBERON:0003701	95.62	gold quality
superficial temporal artery	UBERON:0001614	95.37	gold quality
monocyte	CL:0000576	95.33	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	95.25	gold quality
left uterine tube	UBERON:0001303	95.23	gold quality
body of pancreas	UBERON:0001150	95.22	gold quality
mononuclear cell	CL:0000842	95.17	gold quality
leukocyte	CL:0000738	94.92	gold quality
pancreas	UBERON:0001264	94.82	gold quality
pericardium	UBERON:0002407	94.80	gold quality
hindlimb stylopod muscle	UBERON:0004252	94.41	gold quality
smooth muscle tissue	UBERON:0001135	94.36	gold quality
omental fat pad	UBERON:0010414	94.36	gold quality

Single-cell (SCXA)

Detected in 13 experiment(s), a significant marker in 10.

Experiment	Marker?	Max mean expression
E-MTAB-9154	yes	1113.99
E-GEOD-83139	yes	708.20
E-MTAB-10287	yes	69.75
E-HCAD-8	yes	59.36
E-MTAB-6701	yes	37.36
E-HCAD-11	yes	21.46
E-GEOD-134144	yes	9.55
E-MTAB-6678	yes	8.52
E-HCAD-10	yes	8.06
E-GEOD-98556	no	907.51
E-MTAB-7008	no	812.58
E-MTAB-3929	no	390.77
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NFE2L2

Literature-anchored findings (GeneRIF, showing 40)

• Data indicate that the reduced vimentin expression in response to EPHB4, WIPF2 and MTHFD2 silencing was observed at mRNA and protein levels. (PMID:23295955)
• The highest scoring pathway is mitochondrial one-carbon metabolism and is centred on MTHFD2. (PMID:24451681)
• Data indicate that methylenetetrahydrofolate dehydrogenase (NADP + -dependent) 2 (MTHFD2)was differentially expressed in breast cancer tissue, suggesting as a prognostic factor and a potential therapeutic target for future breast cancer treatments. (PMID:24870594)
• These findings suggest a previously unknown role for MTHFD2 in cancer cell proliferation, adding to its known function in mitochondrial folate metabolism. (PMID:26461067)
• siRNA-mediated silencing of MTHFD2 inhibited migration, invasion and epithelial-mesenchymal transition progression in hepatocellular carcinoma (HCC) cell lines, but no obvious effects on cell proliferation, apoptosis or cell cycle distribution were detected. MTHFD2 is overexpressed in HCC, and is associated with poor prognosis and cellular features connected to metastatic disease. (PMID:27257051)
• metabolic alterations in MCF7 cells observed as a consequence of MTHFD2 suppression (PMID:27315223)
• Mechanistically, MYC regulates the expression of MTHFD2, and MTHFD2 knockdown suppresses the TCA cycle. (PMID:27325891)
• crystal structure of MTHFD2 in complex with a substrate-based inhibitor and the enzyme cofactors NAD(+) and inorganic phosphate. (PMID:27899380)
• miR-92a inhibits proliferation and induces apoptosis by directly regulating MTHFD2 expression in AML. (PMID:28059050)
• endothelial cells undergo MTHFD2-mediated reprogramming toward serine-glycine and mitochondrial one-carbon metabolism to compensate for the loss of ATP in response to oxidized phospholipids during atherosclerosis (PMID:29895827)
• Knocking down MTHFD2 expression in renal cell carcinoma cells, decreased cell proliferation, migration, and invasion were observed and accompanied by the reduced expression of vimentin. (PMID:30466107)
• Therapies targeting MTHFD2 may eradicate tumors and prevent recurrence. (PMID:30532069)
• MicroRNA-33a-5p suppresses colorectal cancer cell growth by inhibiting MTHFD2. (PMID:31209892)
• MTHFD2 links RNA methylation status to the metabolic state of tumor cells in Renal Cell Carcinoma. (PMID:31289360)
• Cancer cells retain expression of both MTHFD isozymes, but only MTHFD2 displays prominent upregulation in cancer. (PMID:31377316)
• Combinatorial targeting of MTHFD2 and PAICS in purine synthesis as a novel therapeutic strategy. (PMID:31624245)
• Down-regulation of MTHFD2 inhibits NSCLC progression by suppressing cycle-related genes. (PMID:31778025)
• High Expression of Methylenetetrahydrofolate Dehydrogenase 2 (MTHFD2) in Esophageal Squamous Cell Carcinoma and its Clinical Prognostic Significance. (PMID:32088725)
• Detection and characterisation of novel alternative splicing variants of the mitochondrial folate enzyme MTHFD2. (PMID:32880830)
• Identification of MTHFD2 as a novel prognosis biomarker in esophageal carcinoma patients based on transcriptomic data and methylation profiling. (PMID:32925794)
• Clinical significance of circ-MTHFD2 in diagnosis, pathological staging and prognosis of NSCLC. (PMID:33015789)
• Glioma cells require one-carbon metabolism to survive glutamine starvation. (PMID:33468252)
• The folate cycle enzyme MTHFD2 induces cancer immune evasion through PD-L1 up-regulation. (PMID:33782411)
• MTHFD2 promotes tumorigenesis and metastasis in lung adenocarcinoma by regulating AKT/GSK-3beta/beta-catenin signalling. (PMID:34121323)
• MTHFD2 promotes ovarian cancer growth and metastasis via activation of the STAT3 signaling pathway. (PMID:34231329)
• p53 deficiency induces MTHFD2 transcription to promote cell proliferation and restrain DNA damage. (PMID:34244426)
• Non-metabolic function of MTHFD2 activates CDK2 in bladder cancer. (PMID:34632667)
• Up-regulation of MTHFD2 is associated with clinicopathological characteristics and poor survival in ovarian cancer, possibly by regulating MOB1A signaling. (PMID:35135596)
• Pharmacological targeting of MTHFD2 suppresses acute myeloid leukemia by inducing thymidine depletion and replication stress. (PMID:35228749)
• Deacetylation of MTHFD2 by SIRT4 senses stress signal to inhibit cancer cell growth by remodeling folate metabolism. (PMID:35349697)
• [Association of maternal MTHFD1 and MTHFD2 gene polymorphisms with congenital heart disease in offspring].", trans “MTHFD1MTHFD2. (PMID:35894196)
• ATF4/MYC Regulates MTHFD2 to Promote NSCLC Progression by Mediating Redox Homeostasis. (PMID:36051358)
• Folate enzyme MTHFD2 links one-carbon metabolism to unfolded protein response in glioblastoma. (PMID:36089117)
• Metabolic collateral lethal target identification reveals MTHFD2 paralogue dependency in ovarian cancer. (PMID:36131208)
• MTHFD2 suppresses glioblastoma progression via the inhibition of ERK1/2 phosphorylation. (PMID:36493392)
• Upregulation of MTHFD2 is associated with PDL1 activation in bladder cancer via the PI3K/AKT pathway. (PMID:36601741)
• SNHG3/hsa-miR-455-5p Axis-mediated High Expression of MTHFD2 Correlates with Tumor Immune Infiltration and Endometrial Carcinoma Progression. (PMID:37484807)
• Downregulation of MTHFD2 Inhibits Proliferation and Enhances Chemosensitivity in Hepatocellular Carcinoma via PI3K/AKT Pathway. (PMID:38287824)
• Implications of MTHFD2 expression in renal cell carcinoma aggressiveness. (PMID:38422037)
• MTHFD2-mediated redox homeostasis promotes gastric cancer progression under hypoxic conditions. (PMID:38723197)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
mus_musculus	Mthfd2	ENSMUSG00000005667
rattus_norvegicus	Mthfd2	ENSRNOG00000010833
drosophila_melanogaster	pug	FBGN0020385
caenorhabditis_elegans		WBGENE00000929
caenorhabditis_elegans		WBGENE00019492

Paralogs (3): MTHFD1 (ENSG00000100714), MTHFD1L (ENSG00000120254), MTHFD2L (ENSG00000163738)

Protein

Protein identifiers

Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial — P13995 (reviewed: P13995)

All UniProt accessions (10): P13995, A0A7I2V2G4, A0A7I2V2U6, A0A7I2V3T1, A0A7I2V482, A0A7I2YQD4, B8ZZU9, B9A062, F8WF06, F8WF89

UniProt curated annotations — full annotation on UniProt →

Function. Although its dehydrogenase activity is NAD-specific, it can also utilize NADP at a reduced efficiency.

Subunit / interactions. Homodimer.

Subcellular location. Mitochondrion.

Miscellaneous. This NAD-dependent bifunctional enzyme has very different kinetic properties than the larger NADP-dependent trifunctional enzyme and is unique in that it requires formation of an enzyme-magnesium complex to allow binding of NAD.

Similarity. Belongs to the tetrahydrofolate dehydrogenase/cyclohydrolase family.

Isoforms (2)

UniProt ID	Names	Canonical?
P13995-1	1	yes
P13995-2	2

RefSeq proteins (2): NP_001397121, NP_006627* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000672	THF_DH/CycHdrlase	Family
IPR020630	THF_DH/CycHdrlase_cat_dom	Domain
IPR020631	THF_DH/CycHdrlase_NAD-bd_dom	Domain
IPR020867	THF_DH/CycHdrlase_CS	Conserved_site
IPR036291	NAD(P)-bd_dom_sf	Homologous_superfamily
IPR046346	Aminoacid_DH-like_N_sf	Homologous_superfamily

Pfam: PF00763, PF02882

Enzyme classification (BRENDA):

• EC 1.5.1.15 — methylenetetrahydrofolate dehydrogenase (NAD+) (BRENDA: 20 organisms, 33 substrates, 7 inhibitors, 59 Km, 21 kcat entries)
• EC 1.5.1.5 — methylenetetrahydrofolate dehydrogenase (NADP+) (BRENDA: 24 organisms, 41 substrates, 41 inhibitors, 70 Km, 28 kcat entries)
• EC 3.5.4.9 — methenyltetrahydrofolate cyclohydrolase (BRENDA: 53 organisms, 34 substrates, 29 inhibitors, 57 Km, 13 kcat entries)

Substrate kinetics (BRENDA)

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

Substrate	Km (mM)	Measurements
5,10-METHENYLTETRAHYDROFOLATE	0.0045–2.36	30
NADP+	0.0004–0.69	23
5,10-METHYLENETETRAHYDROFOLATE	0.0011–4.76	20
10-FORMYLTETRAHYDROFOLATE	0.009–0.47	14
NAD+	0.013–4	13
NADH	0.0035–2	10
METHENYLTETRAHYDROFOLATE	0.019–0.23	7
L-5,10-METHYLENETETRAHYDROFOLATE	0.0046–0.26	6
NADP+	0.255–2.12	6
5,10-METHENYLTETRAHYDROFOLATE	0.0632–1	5
5,10-METHYLENETETRAHYDROFOLATE	0.0004–0.29	5
5,10-METHENYLTETRAHYDROFOLATE	0.068–0.302	5
5,10-METHYLENETETRAHYDROPTEROYLPOLY-L-GLUTAMATE	0.04–0.153	4
MG2+	0.171–0.25	3
5,10-METHYLENETETRAHYDROPTEROYLGLUTAMATE	0.123–0.133	2

Catalyzed reactions (Rhea), 2 shown:

• (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NAD(+) = (6R)-5,10-methenyltetrahydrofolate + NADH (RHEA:22892)
• (6R)-5,10-methenyltetrahydrofolate + H2O = (6R)-10-formyltetrahydrofolate + H(+) (RHEA:23700)

UniProt features (50 total): helix 12, strand 12, mutagenesis site 10, binding site 5, turn 4, sequence conflict 2, transit peptide 1, chain 1, modified residue 1, cross-link 1, splice variant 1

Structure

Experimental structures (PDB)

16 structures.

PDB	Method	Resolution (Å)
5TC4	X-RAY DIFFRACTION	1.89
6S4E	X-RAY DIFFRACTION	1.9
6S4A	X-RAY DIFFRACTION	1.95
9IT6	X-RAY DIFFRACTION	2.04
9IT3	X-RAY DIFFRACTION	2.06
9IS9	X-RAY DIFFRACTION	2.12
7EHM	X-RAY DIFFRACTION	2.13
7EHJ	X-RAY DIFFRACTION	2.16
6S4F	X-RAY DIFFRACTION	2.2
6JIB	X-RAY DIFFRACTION	2.25
6KG2	X-RAY DIFFRACTION	2.25
7EHN	X-RAY DIFFRACTION	2.25
9ITA	X-RAY DIFFRACTION	2.35
6JID	X-RAY DIFFRACTION	2.5
9ISC	X-RAY DIFFRACTION	2.54
7EHV	X-RAY DIFFRACTION	2.61

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P13995-F1	89.66	0.82

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 (5): 84–88; 131–133; 200–202; 233; 309–313

Post-translational modifications (2): 50, 50

Mutagenesis-validated functional residues (10):

Position	Phenotype
168	significant loss of nad and nadp-dependent dehydrogenase specific activity.
168	complete loss of nad and nadp-dependent dehydrogenase specific activity.
168	80% decrease in nad-dependent dehydrogenase specific activity. 18% decrease in nadp-dependent dehydrogenase specific act
168	82% decrease in nad-dependent dehydrogenase specific activity. 65% decrease in nadp-dependent dehydrogenase specific act
201	complete loss of nad and nadp-dependent dehydrogenase specific activity.
225	complete loss of nad and nadp-dependent dehydrogenase specific activity.
225	84% decrease in nad-dependent dehydrogenase specific activity. 36% increase in nadp-dependent dehydrogenase specific act
233	significant loss of nad and nadp-dependent dehydrogenase specific activity.
233	50% decrease in nad and nadp-dependent dehydrogenase specific activity. reduced affinity for magnesium.
233	almost complete loss of nad-dependent dehydrogenase specific activity. 50% decrease in nadp-dependent dehydrogenase spec

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-196757	Metabolism of folate and pterines
R-HSA-1430728	Metabolism
R-HSA-196849	Metabolism of water-soluble vitamins and cofactors
R-HSA-196854	Metabolism of vitamins and cofactors

MSigDB gene sets: 392 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_UP, TSENG_IRS1_TARGETS_UP, MCLACHLAN_DENTAL_CARIES_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, IVANOVA_HEMATOPOIESIS_MATURE_CELL, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_BIOSYNTHETIC_PROCESS, GOBP_DICARBOXYLIC_ACID_METABOLIC_PROCESS, GOLDRATH_ANTIGEN_RESPONSE, PUJANA_CHEK2_PCC_NETWORK, TERAMOTO_OPN_TARGETS_CLUSTER_7

GO Biological Process (7): formate biosynthetic process (GO:0015943), tetrahydrofolate interconversion (GO:0035999), tetrahydrofolate metabolic process (GO:0046653), folic acid metabolic process (GO:0046655), one-carbon metabolic process (GO:0006730), folic acid-containing compound metabolic process (GO:0006760), small molecule metabolic process (GO:0044281)

GO Molecular Function (9): magnesium ion binding (GO:0000287), methenyltetrahydrofolate cyclohydrolase activity (GO:0004477), methylenetetrahydrofolate dehydrogenase (NAD+) activity (GO:0004487), methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488), phosphate ion binding (GO:0042301), catalytic activity (GO:0003824), protein binding (GO:0005515), oxidoreductase activity (GO:0016491), hydrolase activity (GO:0016787)

GO Cellular Component (3): obsolete extracellular space (GO:0005615), mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Metabolism of water-soluble vitamins and cofactors	1
Metabolism of vitamins and cofactors	1
Metabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
folic acid-containing compound metabolic process	2
oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor	2
catalytic activity	2
formate metabolic process	1
monocarboxylic acid biosynthetic process	1
one-carbon metabolic process	1
tetrahydrofolate metabolic process	1
dicarboxylic acid metabolic process	1
small molecule metabolic process	1
modified amino acid metabolic process	1
pteridine-containing compound metabolic process	1
metabolic process	1
metal ion binding	1
cyclohydrolase activity	1
anion binding	1
molecular_function	1
binding	1
cytoplasm	1
intracellular membrane-bounded organelle	1
mitochondrion	1
intracellular organelle lumen	1

Protein interactions and networks

STRING

2536 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MTHFD2	GART	P22102	949
MTHFD2	SHMT1	P34896	860
MTHFD2	SHMT2	P34897	839
MTHFD2	ATIC	P31939	790
MTHFD2	GLDC	P23378	778
MTHFD2	TYMS	P04818	709
MTHFD2	GMPS	P49915	706
MTHFD2	ALDH1L2	Q3SY69	701
MTHFD2	MTHFD1L	Q6UB35	690
MTHFD2	DHFR	P00374	678
MTHFD2	PSAT1	Q9Y617	674
MTHFD2	MTHFR	P42898	665
MTHFD2	PSPH	P78330	652
MTHFD2	FPGS	Q05932	625
MTHFD2	PHGDH	O43175	619

IntAct

64 interactions, top by confidence:

A	B	Type	Score
SRP9	SRP72	psi-mi:“MI:0914”(association)	0.730
MTHFD2	HRAS	psi-mi:“MI:0914”(association)	0.730
HRAS	MTHFD2	psi-mi:“MI:0914”(association)	0.730
nef	ACOT8	psi-mi:“MI:0914”(association)	0.710
HRAS	RGL2	psi-mi:“MI:0914”(association)	0.660
MTHFD2	NAGK	psi-mi:“MI:0915”(physical association)	0.560
NRAS	RGL2	psi-mi:“MI:0914”(association)	0.550
ACAA1	PEX7	psi-mi:“MI:0914”(association)	0.530
MTHFD2L	MTHFD2	psi-mi:“MI:0914”(association)	0.530
MTHFD2	ACADL	psi-mi:“MI:0914”(association)	0.530
MAPKAPK2	MTHFD2	psi-mi:“MI:0914”(association)	0.530
HSCB	NDUFS8	psi-mi:“MI:0914”(association)	0.460
MTHFD2	DAPK1	psi-mi:“MI:0407”(direct interaction)	0.440
MTHFD2	NAGK	psi-mi:“MI:0915”(physical association)	0.370
Nek2	WDR46	psi-mi:“MI:0914”(association)	0.350
Lmna	HAUS5	psi-mi:“MI:0914”(association)	0.350
DLD	NFKBIE	psi-mi:“MI:0914”(association)	0.350
DLD	IRS4	psi-mi:“MI:0914”(association)	0.350
MAB21L2	PTBP1	psi-mi:“MI:0914”(association)	0.350
CUL3	PXDNL	psi-mi:“MI:0914”(association)	0.350
LRRK2		psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
S	COPE	psi-mi:“MI:0914”(association)	0.350
SLC16A11	ESYT2	psi-mi:“MI:0914”(association)	0.350
CCP110	A2ML1	psi-mi:“MI:0914”(association)	0.350

BioGRID (143): MTHFD2 (Affinity Capture-MS), NAGK (Two-hybrid), MTHFD2 (Affinity Capture-MS), CLIC1 (Co-fractionation), MTHFD2 (Reconstituted Complex), NAGK (Two-hybrid), MTHFD2 (Affinity Capture-MS), MTHFD2 (Affinity Capture-MS), MTHFD2 (Affinity Capture-MS), MTHFD2 (Affinity Capture-MS), MTHFD2 (Affinity Capture-MS), MTHFD2L (Affinity Capture-MS), MTHFD2 (Affinity Capture-MS), ACADL (Affinity Capture-MS), TFCP2 (Affinity Capture-MS)

ESM2 similar proteins: A0JME6, A6QLY4, B5X0W9, F6HDM2, G4YEI5, O49472, P08030, P09556, P13995, P35914, P47956, P47957, P54886, P54889, P85094, Q01637, Q08C33, Q0P5C2, Q32KX0, Q32LQ3, Q3T099, Q43153, Q4R826, Q54NZ6, Q54NZ8, Q5M8W9, Q5PQ71, Q5R4M8, Q5R9E1, Q5RC03, Q5U3Z3, Q5ZKA5, Q68FS1, Q6DF67, Q6I7R3, Q6NY77, Q8HXZ6, Q8K009, Q8LG77, Q8TB37

Diamond homologs: A0M554, A0RQ49, A1A8J4, A1BF67, A1VZJ8, A2RLU5, A3DEE6, A4SER8, A5FNE3, A5IRV0, A6GZM5, A6L2G2, A6L8J2, A6Q2W6, A6Q815, A6QFS2, A6U0N1, A7GXK2, A7I254, A7MJZ6, A7X0V3, A7ZCH3, A7ZIT8, A7ZXI3, A8ESH8, A8FLR4, A8Z1K5, A8ZTQ4, B1HRX9, B1IZ72, B1LKE8, B1XGC7, B2UM17, B2V9R3, B3ECA6, B3EJG9, B3ESU1, B3QUL4, B4S820, B4SGR4

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
NFE2L2	“up-regulates quantity by expression”	MTHFD2	“transcriptional regulation”
MTHFD2	“up-regulates quantity”	(6R)-5,10-methenyltetrahydrofolate	“chemical modification”
MTHFD2	“up-regulates quantity”	10-formyltetrahydrofolate(2-)	“chemical modification”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 71 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:

Pathway	Partners	Fold	FDR
Regulation of RAS by GAPs	5	20.2×	2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	48
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1701 predictions. Top by Δscore:

Variant	Effect	Δscore
2:74205700:TGCA:T	acceptor_loss	1.0000
2:74205703:A:AG	acceptor_gain	1.0000
2:74205704:G:GA	acceptor_gain	1.0000
2:74205704:GA:G	acceptor_gain	1.0000
2:74205704:GAA:G	acceptor_gain	1.0000
2:74205704:GAAAT:G	acceptor_gain	1.0000
2:74205886:GTGG:G	donor_gain	1.0000
2:74205888:GG:G	donor_gain	1.0000
2:74205889:GG:G	donor_gain	1.0000
2:74205890:G:GG	donor_gain	1.0000
2:74207699:AATAG:A	acceptor_gain	1.0000
2:74207702:A:AG	acceptor_gain	1.0000
2:74207702:A:C	acceptor_loss	1.0000
2:74207703:G:GA	acceptor_loss	1.0000
2:74207703:G:GG	acceptor_gain	1.0000
2:74207823:CCAGG:C	donor_loss	1.0000
2:74207825:AGGT:A	donor_loss	1.0000
2:74207826:GGT:G	donor_loss	1.0000
2:74207827:G:GC	donor_loss	1.0000
2:74207828:T:A	donor_loss	1.0000
2:74208563:TTTCA:T	acceptor_loss	1.0000
2:74208564:TTCA:T	acceptor_loss	1.0000
2:74208565:TCA:T	acceptor_loss	1.0000
2:74208566:CA:C	acceptor_loss	1.0000
2:74208567:A:AG	acceptor_gain	1.0000
2:74208567:A:C	acceptor_loss	1.0000
2:74208568:G:GG	acceptor_gain	1.0000
2:74208568:GA:G	acceptor_gain	1.0000
2:74208568:GAGC:G	acceptor_gain	1.0000
2:74208616:G:GT	donor_gain	1.0000

AlphaMissense

2269 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:74205867:A:C	K88N	0.999
2:74205867:A:T	K88N	0.999
2:74211280:T:A	I251K	0.999
2:74211789:T:A	V271D	0.999
2:74205844:A:C	S81R	0.998
2:74205846:T:A	S81R	0.998
2:74205846:T:G	S81R	0.998
2:74207809:T:A	V131D	0.998
2:74208616:G:C	D153H	0.998
2:74209978:G:A	G200E	0.998
2:74209981:G:T	R201M	0.998
2:74211211:T:A	V228D	0.998
2:74211849:G:A	G291E	0.998
2:74205812:T:C	L70P	0.997
2:74208622:G:C	D155H	0.997
2:74208623:A:T	D155V	0.997
2:74208626:G:A	G156D	0.997
2:74209972:T:A	V198E	0.997
2:74209981:G:C	R201T	0.997
2:74211280:T:G	I251R	0.997
2:74211849:G:T	G291V	0.997
2:74211851:G:C	D292H	0.997
2:74211852:A:T	D292V	0.997
2:74214112:T:A	V308D	0.997
2:74214148:T:C	L320P	0.997
2:74205857:T:A	V85D	0.996
2:74205865:A:G	K88E	0.996
2:74205866:A:T	K88I	0.996
2:74205877:G:C	A92P	0.996
2:74207800:G:A	G128D	0.996

dbSNP variants (sampled 300 via entrez): RS1000277372 (2:74217499 T>G), RS1000372634 (2:74209471 T>C), RS1000710856 (2:74217268 A>G), RS1000792161 (2:74218032 G>T), RS1001042753 (2:74202066 A>G), RS1001105800 (2:74212389 C>T), RS1001138361 (2:74211683 A>C,G), RS1001409300 (2:74208327 G>A), RS1001740925 (2:74217849 G>C), RS1001831458 (2:74213556 C>A,T), RS1001977838 (2:74212512 C>T), RS1002033806 (2:74199729 A>G), RS1002035909 (2:74210765 T>C,G), RS1002255614 (2:74199333 G>A,T), RS1002341593 (2:74206547 G>A)

Disease associations

OMIM: gene MIM:604887 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3621036 (SINGLE PROTEIN)

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

Binding affinities (BindingDB)

35 measured of 35 human assays (35 total across all organisms); most potent 35 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value	Patent
(2S)-2-[[6-cyclopropyloxy-5-[(2,4-diamino-6-oxo-1,3-diazinan-5-yl)carbamoylamino]pyridine-2-carbonyl]amino]pentanedioic acid	IC50	3 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[[(Z)-(4-amino-2-imino-6-oxopyrimidin-5-ylidene)carbamoyl]amino]-3-fluoropyridine-2-carbonyl]amino]-4-(2H-tetrazol-5-yl)butanoic acid	IC50	3 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[(2,4-diamino-6-oxo-1,3-diazinan-5-yl)carbamoylamino]-3-fluoropyridine-2-carbonyl]amino]-3-phenylpropanoic acid	IC50	5 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[[(Z)-(4-amino-2-imino-6-oxopyrimidin-5-ylidene)carbamoyl]amino]-3-fluoropyridine-2-carbonyl]amino]-3-methylbutanoic acid	IC50	8 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[(2,4-diamino-6-oxo-1,3-diazinan-5-yl)carbamoylamino]-3-fluoropyridine-2-carbonyl]amino]pentanedioic acid	IC50	10 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-5-(benzenesulfonamido)-2-[[5-[(2,4-diamino-6-oxo-1,3-diazinan-5-yl)carbamoylamino]pyridine-2-carbonyl]amino]-5-oxopentanoic acid	IC50	11 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[[(Z)-(4-amino-2-imino-6-oxopyrimidin-5-ylidene)carbamoyl]amino]pyridine-2-carbonyl]amino]-4-(2H-tetrazol-5-yl)butanoic acid	IC50	12 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[[2-(4-amino-2-imino-6-oxo-5H-pyrimidin-5-yl)acetyl]amino]-3-fluoropyridine-2-carbonyl]amino]-4-(2H-tetrazol-5-yl)butanoic acid	IC50	13 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[[2-(2,4-diamino-6-oxo-1,3-diazinan-5-yl)acetyl]amino]-6-phenoxypyridine-2-carbonyl]amino]pentanedioic acid	IC50	14 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[[(Z)-(4-amino-2-imino-6-oxopyrimidin-5-ylidene)carbamoyl]amino]-3-chloropyridine-2-carbonyl]amino]pentanedioic acid	IC50	15 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-cyclohexyl-2-[[5-[(2,4-diamino-6-oxo-1,3-diazinan-5-yl)carbamoylamino]pyridine-2-carbonyl]amino]acetic acid	IC50	17 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[(2,4-diamino-6-oxo-1,3-diazinan-5-yl)carbamoylamino]pyridine-2-carbonyl]amino]-3-methylbutanoic acid	IC50	19 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[(2,4-diamino-6-oxo-1,3-diazinan-5-yl)carbamoylamino]pyridine-2-carbonyl]amino]-2-phenylacetic acid	IC50	23 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[(2,4-diamino-6-oxo-1,3-diazinan-5-yl)carbamoylamino]pyridine-2-carbonyl]amino]pentanedioic acid	IC50	24 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2R)-2-[[(4S)-4-carboxy-4-[[5-[(2,4-diamino-6-oxo-1,3-diazinan-5-yl)carbamoylamino]pyridine-2-carbonyl]amino]butanoyl]amino]pentanedioic acid	IC50	30 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[[(Z)-(4-amino-2-imino-6-oxopyrimidin-5-ylidene)carbamoyl]amino]pyridine-2-carbonyl]amino]hexanedioic acid	IC50	32 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[(2,4-diamino-6-oxo-1,3-diazinan-5-yl)carbamoylamino]pyridine-2-carbonyl]amino]-4-phenylbutanoic acid	IC50	36 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[(4S)-4-carboxy-4-[[5-[(2,4-diamino-6-oxo-1,3-diazinan-5-yl)carbamoylamino]pyridine-2-carbonyl]amino]butanoyl]amino]pentanedioic acid	IC50	43 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[[2-(4-amino-2-imino-6-oxo-5H-pyrimidin-5-yl)acetyl]amino]-6-methoxypyridine-2-carbonyl]amino]pentanedioic acid	IC50	44 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-3-cyclopentyl-2-[[5-[(2,4-diamino-6-oxo-1,3-diazinan-5-yl)carbamoylamino]pyridine-2-carbonyl]amino]propanoic acid	IC50	46 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[[2-(2,4-diamino-6-oxo-1,3-diazinan-5-yl)acetyl]amino]-3-fluoropyridine-2-carbonyl]amino]pentanedioic acid	IC50	49 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[[2-(4-amino-2-imino-6-oxo-5H-pyrimidin-5-yl)acetyl]amino]pyridine-2-carbonyl]amino]-4-(2H-tetrazol-5-yl)butanoic acid	IC50	53 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[[2-(4-amino-2-imino-6-oxo-5H-pyrimidin-5-yl)acetyl]amino]-3-fluoropyridine-2-carbonyl]amino]-3-methylbutanoic acid	IC50	60 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[[2-(2,4-diamino-6-oxo-1,3-diazinan-5-yl)acetyl]amino]-6-phenylpyridine-2-carbonyl]amino]pentanedioic acid	IC50	65 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[[(Z)-(4-amino-2-imino-6-oxopyrimidin-5-ylidene)carbamoyl]amino]pyridine-2-carbonyl]amino]-3-phenylpropanoic acid	IC50	68 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[3-chloro-5-[[2-(2,4-diamino-6-oxo-1,3-diazinan-5-yl)acetyl]amino]pyridine-2-carbonyl]amino]pentanedioic acid	IC50	72 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[(4S)-4-carboxy-4-[[5-[[2-(2,4-diamino-6-oxo-1,3-diazinan-5-yl)acetyl]amino]pyridine-2-carbonyl]amino]butanoyl]amino]pentanedioic acid	IC50	92 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[[2-(4-amino-2-imino-6-oxo-5H-pyrimidin-5-yl)acetyl]amino]-3-fluoropyridine-2-carbonyl]amino]-3-phenylpropanoic acid	IC50	92 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[[2-(2,4-diamino-6-oxo-1,3-diazinan-5-yl)acetyl]amino]pyridine-2-carbonyl]amino]-3-methylbutanoic acid	IC50	103 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[[2-(2,4-diamino-6-oxo-1,3-diazinan-5-yl)acetyl]amino]pyridine-2-carbonyl]amino]pentanedioic acid	IC50	154 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[(2,4-diamino-6-oxo-1,3-diazinan-5-yl)carbamoylamino]pyridine-2-carbonyl]amino]butanedioic acid	IC50	195 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[[2-(2,4-diamino-6-oxo-1,3-diazinan-5-yl)acetyl]amino]-6-ethenylpyridine-2-carbonyl]amino]pentanedioic acid	IC50	298 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[[2-(2,4-diamino-6-oxo-1,3-diazinan-5-yl)acetyl]amino]pyridine-2-carbonyl]amino]-3-phenylpropanoic acid	IC50	312 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[[2-(2,4-diamino-6-oxo-1,3-diazinan-5-yl)acetyl]amino]-3-methylpyridine-2-carbonyl]amino]pentanedioic acid	IC50	913 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy
(2S)-2-[[5-[[2-(2,4-diamino-6-oxo-1,3-diazinan-5-yl)acetyl]amino]-3-(trifluoromethyl)pyridine-2-carbonyl]amino]pentanedioic acid	IC50	1100 nM	US-11504368: 2,6-diamino-3,4-dihydropyrimidin-4-one derivatives and use thereof in therapy

ChEMBL bioactivities

60 potent at pChembl≥5 of 63 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
8.20	IC50	6.3	nM	CHEMBL4463968
8.03	IC50	9.3	nM	CHEMBL4470947
7.75	IC50	18	nM	CHEMBL4534641
7.68	IC50	21	nM	CHEMBL4483030
7.66	IC50	22	nM	CHEMBL6133989
7.54	Ki	29	nM	CHEMBL297258
7.48	IC50	33	nM	CHEMBL4542665
7.43	IC50	37	nM	CHEMBL4584730
7.42	IC50	38	nM	CHEMBL4538356
7.40	IC50	40	nM	CHEMBL6103492
7.33	IC50	47	nM	CHEMBL5879031
7.32	IC50	48	nM	CHEMBL4546647
7.31	IC50	49	nM	CHEMBL4441993
7.28	IC50	53	nM	CHEMBL4460077
7.18	IC50	66	nM	CHEMBL6159806
7.10	IC50	80	nM	CHEMBL3622702
7.05	IC50	89	nM	CHEMBL4551634
7.05	IC50	90	nM	CHEMBL6102973
6.89	IC50	130	nM	CHEMBL4474051
6.87	IC50	134	nM	CHEMBL6149895
6.82	IC50	150	nM	CHEMBL6102567
6.72	IC50	190	nM	CHEMBL5076176
6.70	IC50	200	nM	CHEMBL4451401
6.50	IC50	320	nM	CHEMBL4467997
6.47	IC50	340	nM	CHEMBL4526400
6.47	IC50	340	nM	CHEMBL4460238
6.44	IC50	360	nM	CHEMBL4458187
6.41	IC50	390	nM	CHEMBL4472668
6.40	IC50	400	nM	CHEMBL4438430
6.33	IC50	470	nM	CHEMBL6152791
6.28	IC50	530	nM	CHEMBL4592118
6.28	IC50	530	nM	CHEMBL6102503
6.18	IC50	663	nM	CHEMBL1233930
6.16	IC50	690	nM	CHEMBL5090659
6.11	IC50	780	nM	CHEMBL5093943
6.11	IC50	780	nM	CHEMBL5085594
6.04	IC50	910	nM	CHEMBL5084848
6.04	IC50	910	nM	CHEMBL6134698
6.03	IC50	940	nM	CHEMBL4540255
5.89	IC50	1300	nM	CHEMBL4436668
5.85	IC50	1400	nM	CHEMBL4443536
5.80	IC50	1600	nM	CHEMBL4474283
5.72	IC50	1900	nM	CHEMBL4465667
5.64	IC50	2300	nM	CHEMBL4448164
5.57	IC50	2700	nM	CHEMBL4530832
5.51	IC50	3100	nM	CHEMBL4470717
5.42	IC50	3800	nM	CHEMBL4441792
5.40	IC50	4000	nM	CHEMBL5077748
5.34	IC50	4600	nM	CHEMBL4538051
5.21	IC50	6210	nM	CHEMBL5077920

PubChem BioAssay actives

44 with measured affinity, of 78 total; 44 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
N-[4-[8-[(3S)-3,4-dimethylpiperazin-1-yl]-7-methyl-5-oxo-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl]-2-(trifluoromethoxy)phenyl]methanesulfonamide	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	0.0063	uM
N-[2-chloro-4-[8-[(3S)-3,4-dimethylpiperazin-1-yl]-7-methyl-5-oxo-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl]phenyl]methanesulfonamide	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	0.0093	uM
3-(2,2-dioxo-1,3-dihydro-2,1-benzothiazole-5-carbonyl)-7-methyl-8-(4-methylpiperazin-1-yl)-2,4-dihydro-1H-chromeno[3,4-c]pyridin-5-one;2,2,2-trifluoroacetic acid	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	0.0180	uM
N-[4-[7-methyl-8-(4-methylpiperazin-1-yl)-5-oxo-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl]-2-(trifluoromethoxy)phenyl]methanesulfonamide	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	0.0210	uM
2-[[4-(3-amino-1,9-dioxo-5,6,6a,7-tetrahydro-2H-imidazo[1,5-f]pteridin-8-yl)benzoyl]amino]pentanedioic acid	1250600: Competitive inhibition of human FolD dehydrogenase activity	ki	0.0290	uM
N-[2-bromo-4-[7-methyl-8-(4-methylpiperazin-1-yl)-5-oxo-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl]phenyl]methanesulfonamide	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	0.0330	uM
N-[2-chloro-4-[7-methyl-5-oxo-8-[(3S,5R)-3,4,5-trimethylpiperazin-1-yl]-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl]phenyl]methanesulfonamide	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	0.0370	uM
N-[2-fluoro-4-[7-methyl-8-(4-methylpiperazin-1-yl)-5-oxo-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl]phenyl]methanesulfonamide	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	0.0380	uM
N-[2-chloro-4-[7-methyl-8-(4-methylpiperazin-1-yl)-5-oxo-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl]phenyl]methanesulfonamide	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	0.0480	uM
4-[8-[2-(dimethylamino)ethoxy]-7-methyl-5-oxo-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl]benzoic acid;hydrochloride	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	0.0490	uM
8-[2-(dimethylamino)ethoxy]-3-(2,2-dioxo-1,3-dihydro-2,1-benzothiazole-5-carbonyl)-7-methyl-2,4-dihydro-1H-chromeno[3,4-c]pyridin-5-one;2,2,2-trifluoroacetic acid	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	0.0530	uM
N-[3-chloro-5-[7-methyl-8-(4-methylpiperazin-1-yl)-5-oxo-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl]phenyl]methanesulfonamide	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	0.0890	uM
N-[2-chloro-4-[8-[(3R)-3,4-dimethylpiperazin-1-yl]-7-methyl-5-oxo-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl]phenyl]methanesulfonamide	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	0.1300	uM
(2S)-2-[[4-[[1-[(4-chloro-1H-indol-2-yl)methyl]-3,7-dimethyl-2,6-dioxopurin-8-yl]amino]benzoyl]amino]pentanedioic acid	1809111: Inhibition of C-terminal His-tagged human MTHFD2 (36 to 350 residues) expressed in insect cells using tetrahydrofolate as substrate preincubated for 10 min in presence of NAD+ followed by addition of substrate and further incubated for 10 mins	ic50	0.1900	uM
N-[4-[7-methyl-8-(4-methylpiperazin-1-yl)-5-oxo-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl]phenyl]methanesulfonamide	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	0.2000	uM
4-[8-(4-methylpiperazin-1-yl)-5-oxo-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl]benzoic acid	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	0.3200	uM
4-[8-[4-[(dimethylamino)methyl]phenyl]-5-oxo-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl]benzoic acid	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	0.3400	uM
4-[8-[2-(dimethylamino)ethoxy]-5-oxo-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl]benzoic acid	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	0.3400	uM
4-[8-[3-(dimethylamino)propoxy]-5-oxo-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl]benzoic acid	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	0.3600	uM
4-[8-(1-methylpiperidin-4-yl)oxy-5-oxo-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl]benzoic acid	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	0.3900	uM
N-[2-methoxy-4-[7-methyl-8-(4-methylpiperazin-1-yl)-5-oxo-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl]phenyl]methanesulfonamide	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	0.4000	uM
N-[2-methyl-4-[7-methyl-8-(4-methylpiperazin-1-yl)-5-oxo-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl]phenyl]methanesulfonamide	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	0.5300	uM
(2S)-2-[[4-[(6aR)-3-amino-1,9-dioxo-5,6,6a,7-tetrahydro-2H-imidazo[1,5-f]pteridin-8-yl]benzoyl]amino]pentanedioic acid	1634023: Inhibition of His-tagged human MTHFD2 ( 36 to 350 residues) expressed in Escherichia coli BL21 (DE3) pre-incubated for 10 mins before folitixorin and NAD+ addition measured after 15 mins by NAD(P)H-Glo detection reagent based luminescence assay	ic50	0.6630	uM
3-[4-[[1-[(4-chloro-1H-indol-2-yl)methyl]-3,7-dimethyl-2,6-dioxopurin-8-yl]amino]-6-methylpyrimidin-2-yl]propanoic acid	1809111: Inhibition of C-terminal His-tagged human MTHFD2 (36 to 350 residues) expressed in insect cells using tetrahydrofolate as substrate preincubated for 10 min in presence of NAD+ followed by addition of substrate and further incubated for 10 mins	ic50	0.6900	uM
(2S)-2-[[4-[[1-[(3,4-dichlorophenyl)methyl]-3,7-dimethyl-2,6-dioxopurin-8-yl]amino]benzoyl]amino]pentanedioic acid	1809111: Inhibition of C-terminal His-tagged human MTHFD2 (36 to 350 residues) expressed in insect cells using tetrahydrofolate as substrate preincubated for 10 min in presence of NAD+ followed by addition of substrate and further incubated for 10 mins	ic50	0.7800	uM
(2S)-2-[[4-[[1-[(3,4-dichlorophenyl)methyl]-3-methyl-2,6-dioxopyrimidin-4-yl]carbamoylamino]benzoyl]amino]pentanedioic acid	1809111: Inhibition of C-terminal His-tagged human MTHFD2 (36 to 350 residues) expressed in insect cells using tetrahydrofolate as substrate preincubated for 10 min in presence of NAD+ followed by addition of substrate and further incubated for 10 mins	ic50	0.7800	uM
(2S)-2-[[4-[[1-[(3,4-dichlorophenyl)methyl]-3,7-dimethyl-2,6-dioxopurin-8-yl]amino]benzoyl]amino]butanedioic acid	1809111: Inhibition of C-terminal His-tagged human MTHFD2 (36 to 350 residues) expressed in insect cells using tetrahydrofolate as substrate preincubated for 10 min in presence of NAD+ followed by addition of substrate and further incubated for 10 mins	ic50	0.9100	uM
2-chloro-4-(4-oxo-2-phenyl-3,5,7,8-tetrahydropyrido[4,3-d]pyrimidine-6-carbonyl)benzoic acid	1634025: Inhibition of recombinant MTHFD2 (unknown origin) assessed as reduction in methenyl-THF formation using tetrahydrofolate, NAD and formaldehyde incubated for 30 mins by NAD-dependent dehydrogenase assay	ic50	0.9400	uM
4-(10-methyl-5-oxo-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl)benzoic acid	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	1.3000	uM
4-(4-oxo-2-phenyl-3,5,7,8-tetrahydropyrido[4,3-d]pyrimidine-6-carbonyl)naphthalene-1-carboxylic acid	1634025: Inhibition of recombinant MTHFD2 (unknown origin) assessed as reduction in methenyl-THF formation using tetrahydrofolate, NAD and formaldehyde incubated for 30 mins by NAD-dependent dehydrogenase assay	ic50	1.4000	uM
4-(5-oxo-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl)benzoic acid	1634025: Inhibition of recombinant MTHFD2 (unknown origin) assessed as reduction in methenyl-THF formation using tetrahydrofolate, NAD and formaldehyde incubated for 30 mins by NAD-dependent dehydrogenase assay	ic50	1.6000	uM
4-(8-oxo-1,5,9-triazatricyclo[7.4.0.02,7]tridec-2(7)-ene-5-carbonyl)benzoic acid	1634025: Inhibition of recombinant MTHFD2 (unknown origin) assessed as reduction in methenyl-THF formation using tetrahydrofolate, NAD and formaldehyde incubated for 30 mins by NAD-dependent dehydrogenase assay	ic50	1.9000	uM
4-(1-methyl-4-oxo-2-phenyl-7,8-dihydro-5H-1,6-naphthyridine-6-carbonyl)benzoic acid	1634025: Inhibition of recombinant MTHFD2 (unknown origin) assessed as reduction in methenyl-THF formation using tetrahydrofolate, NAD and formaldehyde incubated for 30 mins by NAD-dependent dehydrogenase assay	ic50	2.3000	uM
4-(4-oxo-2-phenyl-3,5,7,8-tetrahydropyrido[4,3-d]pyrimidine-6-carbonyl)benzoic acid	1634025: Inhibition of recombinant MTHFD2 (unknown origin) assessed as reduction in methenyl-THF formation using tetrahydrofolate, NAD and formaldehyde incubated for 30 mins by NAD-dependent dehydrogenase assay	ic50	2.7000	uM
2-amino-4-(4-oxo-2-phenyl-3,5,7,8-tetrahydropyrido[4,3-d]pyrimidine-6-carbonyl)benzoic acid	1634025: Inhibition of recombinant MTHFD2 (unknown origin) assessed as reduction in methenyl-THF formation using tetrahydrofolate, NAD and formaldehyde incubated for 30 mins by NAD-dependent dehydrogenase assay	ic50	3.1000	uM
4-[8-[4-(dimethylamino)phenyl]-5-oxo-2,4-dihydro-1H-chromeno[3,4-c]pyridine-3-carbonyl]benzoic acid	1541133: Inhibition of recombinant MTHFD2 (unknown origin) using THF as substrate incubated for 30 mins in presence of NAD	ic50	3.8000	uM
1-[(3,4-dichlorophenyl)methyl]-8-[(4-hydroxycyclohexyl)amino]-3,7-dimethylpurine-2,6-dione	1809111: Inhibition of C-terminal His-tagged human MTHFD2 (36 to 350 residues) expressed in insect cells using tetrahydrofolate as substrate preincubated for 10 min in presence of NAD+ followed by addition of substrate and further incubated for 10 mins	ic50	4.0000	uM
4-(5-oxo-1,2,4,6-tetrahydrobenzo[f][2,7]naphthyridine-3-carbonyl)benzoic acid	1634025: Inhibition of recombinant MTHFD2 (unknown origin) assessed as reduction in methenyl-THF formation using tetrahydrofolate, NAD and formaldehyde incubated for 30 mins by NAD-dependent dehydrogenase assay	ic50	4.6000	uM
4-[[1-[(3,4-dichlorophenyl)methyl]-3-methyl-2,6-dioxopyrimidin-4-yl]carbamoylamino]benzoic acid	1809111: Inhibition of C-terminal His-tagged human MTHFD2 (36 to 350 residues) expressed in insect cells using tetrahydrofolate as substrate preincubated for 10 min in presence of NAD+ followed by addition of substrate and further incubated for 10 mins	ic50	6.2100	uM
4-(7-oxo-2,6,10-triazatricyclo[6.4.0.02,6]dodec-1(8)-ene-10-carbonyl)benzoic acid	1634025: Inhibition of recombinant MTHFD2 (unknown origin) assessed as reduction in methenyl-THF formation using tetrahydrofolate, NAD and formaldehyde incubated for 30 mins by NAD-dependent dehydrogenase assay	ic50	6.6000	uM
4-(2-oxo-1,5,9-triazatricyclo[8.4.0.03,8]tetradeca-3(8),9-diene-5-carbonyl)benzoic acid	1634025: Inhibition of recombinant MTHFD2 (unknown origin) assessed as reduction in methenyl-THF formation using tetrahydrofolate, NAD and formaldehyde incubated for 30 mins by NAD-dependent dehydrogenase assay	ic50	8.2000	uM
6-(2,2-dioxo-1,3-dihydro-2,1-benzothiazole-5-carbonyl)-2-phenyl-3,5,7,8-tetrahydropyrido[4,3-d]pyrimidin-4-one	1634025: Inhibition of recombinant MTHFD2 (unknown origin) assessed as reduction in methenyl-THF formation using tetrahydrofolate, NAD and formaldehyde incubated for 30 mins by NAD-dependent dehydrogenase assay	ic50	8.3000	uM
2-phenyl-6-[4-(2H-tetrazol-5-yl)benzoyl]-3,5,7,8-tetrahydropyrido[4,3-d]pyrimidin-4-one	1634025: Inhibition of recombinant MTHFD2 (unknown origin) assessed as reduction in methenyl-THF formation using tetrahydrofolate, NAD and formaldehyde incubated for 30 mins by NAD-dependent dehydrogenase assay	ic50	10.0000	uM
5-(4-oxo-2-phenyl-3,5,7,8-tetrahydropyrido[4,3-d]pyrimidine-6-carbonyl)pyridine-2-carboxylic acid	1634025: Inhibition of recombinant MTHFD2 (unknown origin) assessed as reduction in methenyl-THF formation using tetrahydrofolate, NAD and formaldehyde incubated for 30 mins by NAD-dependent dehydrogenase assay	ic50	10.0000	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases methylation, decreases expression, increases expression	6
Cyclosporine	affects expression, increases expression	6
Particulate Matter	affects expression, decreases expression, increases abundance, increases expression, affects cotreatment	6
sodium arsenite	affects methylation, affects binding, increases reaction, decreases methylation, increases expression	5
Tunicamycin	increases expression	5
methylmercuric chloride	increases expression, affects cotreatment	4
Air Pollutants	affects expression, increases abundance, increases expression, affects cotreatment, decreases expression	4
Tetrachlorodibenzodioxin	affects cotreatment, increases expression, decreases expression	4
Valproic Acid	affects expression, decreases expression	4
bisphenol A	affects expression, decreases expression, increases expression	3
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression, increases expression	2
Acetaminophen	affects expression, increases expression	2
Carbamazepine	affects expression	2
Cisplatin	increases expression, decreases response to substance	2
Nickel	increases expression	2
Tretinoin	decreases expression	2
Asbestos, Crocidolite	affects expression, increases expression	2
Thapsigargin	increases expression	2
pirinixic acid	affects binding, increases activity, increases expression	1
deoxynivalenol	decreases expression	1
beta-lapachone	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
nickel chloride	increases expression	1
perfluorooctanoic acid	increases expression	1
sulindac sulfide	increases expression	1
coumarin	increases phosphorylation	1
quinoline	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression	1
beta-methylcholine	affects expression	1
perfluorooctane sulfonic acid	increases expression	1

ChEMBL screening assays

17 unique, capped per target: 17 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL3626666	Binding	Competitive inhibition of human FolD dehydrogenase activity	Characterization of 2,4-Diamino-6-oxo-1,6-dihydropyrimidin-5-yl Ureido Based Inhibitors of Trypanosoma brucei FolD and Testing for Antiparasitic Activity. — J Med Chem

Cellosaurus cell lines

4 cell lines: 3 cancer cell line, 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B3BF	Abcam HEK293T MTHFD2 KO	Transformed cell line	Female
CVCL_SZ21	HAP1 MTHFD2 (-) 1	Cancer cell line	Male
CVCL_XQ75	HAP1 MTHFD2 (-) 2	Cancer cell line	Male
CVCL_XQ76	HAP1 MTHFD2 (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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