TYMS

Summary

TYMS (thymidylate synthetase, HGNC:12441) is a protein-coding gene on chromosome 18p11.32, encoding Thymidylate synthase (P04818). Catalyzes the reductive methylation of 2’-deoxyuridine 5’-monophosphate (dUMP) to thymidine 5’-monophosphate (dTMP), using the cosubstrate, 5,10- methylenetetrahydrofolate (CH2H4folate) as a 1-carbon donor and reductant and contributes to the mitochondrial and nuclear de novo th…. In precision oncology, TYMS Underexpression confers sensitivity to Pemetrexed in Lung Non-small Cell Carcinoma (CIViC Level B); 7 further curated variant–drug associations are listed below. It is a selective cancer dependency (DepMap: 50.8% of cell lines).

Thymidylate synthase catalyzes the methylation of deoxyuridylate to deoxythymidylate using, 10-methylenetetrahydrofolate (methylene-THF) as a cofactor. This function maintains the dTMP (thymidine-5-prime monophosphate) pool critical for DNA replication and repair. The enzyme has been of interest as a target for cancer chemotherapeutic agents. It is considered to be the primary site of action for 5-fluorouracil, 5-fluoro-2-prime-deoxyuridine, and some folate analogs. Expression of this gene and that of a naturally occurring antisense transcript, mitochondrial enolase superfamily member 1 (GeneID:55556), vary inversely when cell-growth progresses from late-log to plateau phase. Polymorphisms in this gene may be associated with etiology of neoplasia, including breast cancer, and response to chemotherapy.

Source: NCBI Gene 7298 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 27 total — 2 pathogenic
• Phenotypes (HPO): 84
• Druggable target: yes — 9 molecules with ChEMBL bioactivity
• Precision-oncology evidence (CIViC): 8 curated variant–drug associations
• Cancer dependency (DepMap): dependent in 50.8% of screened cell lines
• MANE Select transcript: NM_001071

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12441
Approved symbol	TYMS
Name	thymidylate synthetase
Location	18p11.32
Locus type	gene with protein product
Status	Approved
Aliases	Tsase, TMS, HsT422
Ensembl gene	ENSG00000176890
Ensembl biotype	protein_coding
OMIM	188350
Entrez	7298

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000323224, ENST00000323250, ENST00000323274, ENST00000579128, ENST00000581920, ENST00000584122, ENST00000918013, ENST00000918014

RefSeq mRNA: 3 — MANE Select: NM_001071 NM_001071, NM_001354867, NM_001354868

CCDS: CCDS11821, CCDS86658, CCDS86659

Canonical transcript exons

ENST00000323274 — 7 exons

Exon	Start	End
ENSE00001753233	657653	657947
ENSE00002689316	672860	673578
ENSE00003483247	662146	662320
ENSE00003511087	671380	671451
ENSE00003521550	670692	670867
ENSE00003556949	659641	659714
ENSE00003679046	669072	669173

Expression profiles

Bgee: expression breadth ubiquitous, 262 present calls, max score 98.54.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 40.8936 / max 411.1924, expressed in 1722 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
169059	32.3914	1630
169058	4.6952	1211
169057	1.8816	961
169061	0.9502	629
169060	0.6055	398
169065	0.2589	119
169063	0.0763	11
169062	0.0345	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	98.54	gold quality
embryo	UBERON:0000922	98.49	gold quality
trabecular bone tissue	UBERON:0002483	98.33	gold quality
ganglionic eminence	UBERON:0004023	98.06	gold quality
secondary oocyte	CL:0000655	97.51	gold quality
bone marrow	UBERON:0002371	96.37	gold quality
endometrium epithelium	UBERON:0004811	95.85	gold quality
adult organism	UBERON:0007023	95.64	gold quality
oocyte	CL:0000023	95.12	gold quality
cartilage tissue	UBERON:0002418	94.94	gold quality
mucosa of transverse colon	UBERON:0004991	94.57	gold quality
left testis	UBERON:0004533	94.48	gold quality
right testis	UBERON:0004534	94.33	gold quality
rectum	UBERON:0001052	93.97	gold quality
testis	UBERON:0000473	93.70	gold quality
tibia	UBERON:0000979	93.66	gold quality
ileal mucosa	UBERON:0000331	93.60	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	93.55	gold quality
vermiform appendix	UBERON:0001154	93.32	gold quality
bone marrow cell	CL:0002092	93.21	gold quality
colonic mucosa	UBERON:0000317	92.99	gold quality
mucosa of sigmoid colon	UBERON:0004993	92.90	gold quality
thymus	UBERON:0002370	92.77	gold quality
stromal cell of endometrium	CL:0002255	92.74	gold quality
oral cavity	UBERON:0000167	92.06	gold quality
amniotic fluid	UBERON:0000173	91.96	gold quality
caecum	UBERON:0001153	91.92	gold quality
esophagus squamous epithelium	UBERON:0006920	91.80	gold quality
placenta	UBERON:0001987	91.15	gold quality
epithelium of esophagus	UBERON:0001976	91.14	gold quality

Single-cell (SCXA)

Detected in 48 experiment(s), a significant marker in 45.

Experiment	Marker?	Max mean expression
E-HCAD-6	yes	920.59
E-MTAB-8221	yes	802.15
E-MTAB-10432	yes	797.80
E-MTAB-9906	yes	796.41
E-MTAB-10662	yes	792.53
E-MTAB-11121	yes	784.44
E-MTAB-10485	yes	713.90
E-MTAB-6505	yes	698.18
E-GEOD-114530	yes	691.97
E-HCAD-15	yes	684.48
E-MTAB-9435	yes	662.89
E-MTAB-10553	yes	641.49
E-MTAB-8894	yes	637.77
E-MTAB-8142	yes	625.19
E-GEOD-149689	yes	561.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): APBB2, APBB3, CHD8, E2F1, E2F4, ESR1, MYC, NFE2, SMARCA1, SP1, TFCP2, TFDP1, TP53, USF1, YBX1

miRNA regulators (miRDB)

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

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-4639-5P	99.81	67.37	1028
HSA-MIR-4310	99.59	68.84	2527
HSA-MIR-203A-3P	99.49	70.56	2806
HSA-MIR-3978	99.24	68.39	2201
HSA-MIR-4279	99.19	66.70	2437
HSA-MIR-935	98.82	69.36	1072
HSA-MIR-1248	98.47	67.54	1314
HSA-MIR-6736-3P	96.98	65.22	1342
HSA-MIR-6834-5P	96.25	64.88	823
HSA-MIR-4513	95.04	67.06	727
HSA-MIR-6855-3P	95.04	66.57	725
HSA-MIR-5195-5P	90.84	65.09	287

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 50.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 40)

• liganded crystal structures with pyrrolo(2,3-d)pyrimidine-based antifolate compounds (PMID:11697906)
• high level of expression associated with poor prognosis in p-stage I adenocarcinoma of the lung (PMID:11804689)
• Length polymorphism of thymidylate synthase regulatory region in Chinese populations and evolution of the novel alleles (PMID:11989786)
• TK1 gene expression together with TS, TP and DPD gene expression may play important roles in influencing the malignant behavior of epithelial ovarian cancer. (PMID:11992400)
• Mutants of TS that confer resistance to MTX as well as 5-FU by random as well as site-directed mutagenesis. Review. (PMID:12084458)
• Thymidylate synthase as a translational regulator of cellular gene expression. Review. (PMID:12084459)
• rTS gene expression likely plays a role in down-regulating TS through a natural RNA-based antisense mechanism. Review. (PMID:12084460)
• Induction of thymidylate synthase as a 5-fluorouracil resistance mechanism. Review. (PMID:12084461)
• Structure-based studies on species-specific inhibition of thymidylate synthase. Review. (PMID:12084462)
• mutations in TS result in conformational changes that confer 5-fluordeoxyuridine resistance (PMID:12147691)
• TYMS and MTHFR compete for limiting supplies of folate required for the remethylation of homocysteine. (PMID:12215845)
• the identified highly conserved protein domains, which occur at the homodimeric interface of thymidylate synthase(TS), represent potential participating sites for binding of TS protein to its mRNA. (PMID:12220503)
• Enhanced expression mediates resistance of uterine cervical cancer cells to radiation (PMID:12239455)
• cytomegalovirus infection induces cellular thymidylate synthase gene expression in quiescent human embryonic lung fibroblasts (PMID:12466474)
• Gene expression is a predictor for the efficacy of fluoropyrimidine-based chemotherapy for metastatic colorectal cancer. (PMID:12576451)
• Expression predicts the reponse of metastatic colorectal cancer to raltitrexel. (PMID:12576452)
• Associations between polymorphisms in the thymidylate synthase and serine hydroxymethyltransferase genes and susceptibility to malignant lymphoma. (PMID:12604405)
• polymorphism and overexpression of Thymidylate synthase mrna is associated with non-small-cell lung cancer (PMID:12640689)
• Results suggest that the genotyping for thymidylate synthase and methylenetetrahydrofolate reductase polymorphisms may be a useful indicator in determining the appropriate dose of methotrexate in patients with rheumatoid arthritis. (PMID:12684695)
• Overexpression of thymidylate synthase mediates desensitization for 5-fluorouracil of cervical cancer cells (PMID:12845668)
• Results describe the kinetic parameters of human recombinant thymidylate synthase (hrTS) with its natural substrate, dUMP, and E-5-(2-bromovinyl)-2(’)-deoxyuridine monophosphate (BVdUMP). (PMID:12859954)
• Findings identify Cys-180 as a critical residue for the in vitro and in vivo translational regulatory effects of human thymidylate synthase. (PMID:12907731)
• TS and DPD quantitation may be helpful to evaluate prognosis of patients receiving adjuvant 5-FU and that patients with high TS and low DPD may benefit from adjuvant 5-FU chemotherapy in colorectal cancer. (PMID:14519634)
• High TS expression is a marker of poor prognosis in resected pancreatic cancer. Patients with high intratumoral TS expression benefit from adjuvant therapy. (PMID:14519641)
• These results indicate that postoperative chemotherapy with 5-FU could be effective for patients with the G-phenotype tumor, since the incidence of intratumoral expression of TS, the target enzyme of 5-FU, is significantly low in G-phenotype tumors (PMID:14576935)
• There is prognostic significance to TS mRNA expression in breast neoplasms. (PMID:14702180)
• thymidylate synthase loss of heterozygosity has a role in progression of colorectal cancer (PMID:14760062)
• Molecular features of thymidylate synthase that control its degradation are examined; the carboxyl-terminal conformational shift is not required for ligand-mediated stabilization; the amino-terminus governs TS stability and its response to ligands. (PMID:14967037)
• TYMS gene amplification in 23% of 31 5-FU-treated cancers, whereas no amplification was observed in metastases of patients that had not been treated with 5-FU. (PMID:14970324)
• Over expression of Thymidylate synthase exhibits oncogene-like activity and suggest a link between DNA synthesis and the induction of a neoplastic phenotype (PMID:15093541)
• 6 bp/1494 polymorphism varies greatly within different ethnic populations and is in linkage disequilibrium with the thymidylate synthase 5’ tandem repeat enhancer polymorphism (PMID:15115918)
• thymidylate synthase and p53 have roles in regulating Fas-mediated apoptosis in response to antimetabolites (PMID:15161716)
• Polymorphism of TYMS partially modifies the risk of esophageal and stomach cancer in patients with smoking habit. (PMID:15244514)
• Thymidylate synthase inhibition triggers glucose-dependent apoptosis in p53-negative leukemic cells (PMID:15251465)
• The combination of low expression of TS and induction of p16(INK4a) after chemotherapy can be important indicators of the sensitivity to 5-FU-based chemotherapy in colorectal cancers. (PMID:15260847)
• Thymidylate synthase polymorphisms are associated with esophageal squamous cell carcinoma and gastric cardiac adenocarcinoma (PMID:15284183)
• TS in malignant tissue was statistically higher than in normal stromal tissue in both differentiated and undifferentiated types (p < 0.0001). (PMID:15316940)
• Polymorphisms in the TS gene may contribute to gastric cancer susceptibility. (PMID:15386366)
• Polymorphisms of reduced folate carrier,aminoimidazole carboxamide ribonucleotide transformylase,and thymidylate synthase genes contribute to the therapeutic response in rheumatoid arthritis patients to methotrexate. (PMID:15457444)
• The common MTHFR C677T and TS enhancer region polymorphisms were not risk factors for breast cancer in this patient cohort nor were they associated with phenotypic features or with prognosis. (PMID:15510613)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	tyms	ENSDARG00000042894
mus_musculus	Tyms	ENSMUSG00000025747
rattus_norvegicus	Tyms	ENSRNOG00000037225
drosophila_melanogaster	Ts	FBGN0024920
caenorhabditis_elegans	tyms-1	WBGENE00022455

Paralogs (2): DHFR2 (ENSG00000178700), DHFR (ENSG00000228716)

Protein

Protein identifiers

Thymidylate synthase — P04818 (reviewed: P04818)

All UniProt accessions (2): P04818, Q53Y97

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the reductive methylation of 2’-deoxyuridine 5’-monophosphate (dUMP) to thymidine 5’-monophosphate (dTMP), using the cosubstrate, 5,10- methylenetetrahydrofolate (CH2H4folate) as a 1-carbon donor and reductant and contributes to the mitochondrial and nuclear de novo thymidylate biosynthesis pathway.

Subunit / interactions. Homodimer. Part of the de novo thymidylate synthesis complex composed at least by SHMT1, DHFR and TYMS. Interacts with SHMT1; this interaction is DNA-dependent and mediates TYMS co-localization with LMNB1.

Subcellular location. Nucleus. Cytoplasm. Mitochondrion. Mitochondrion matrix. Mitochondrion inner membrane.

Post-translational modifications. Sumoylated by UBE2I/UBC9.

Disease relevance. Dyskeratosis congenita, digenic (DKCD) [MIM:620040] A form of dyskeratosis congenita, a rare multisystem disorder caused by defective telomere maintenance. It is characterized by progressive bone marrow failure, and the clinical triad of reticulated skin hyperpigmentation, nail dystrophy, and mucosal leukoplakia. Common but variable features include premature graying, aplastic anemia, low platelets, osteoporosis, pulmonary fibrosis, and liver fibrosis among others. Early mortality is often associated with bone marrow failure, infections, fatal pulmonary complications, or malignancy. DKCD transmission pattern is consistent with digenic inheritance. The disease is caused by variants affecting distinct genetic loci, including the gene represented in this entry. TYMS germline variants in the presence of a common ENOSF1 haplotype (defined by rs699517, rs2790 and rs1512643) result in severe thymidylate synthase deficiency and disease. The pathogenic mechanism involves increased expression of ENOSF1 relative to TYMS, and post-transcriptional inhibition of TYMS translation through ENOSF1-TYMS RNA-RNA interactions.

Pathway. Pyrimidine metabolism; dTTP biosynthesis.

Miscellaneous. Expressed both in normal and cancerous tissues. Expressed only in cancerous tissues.

Similarity. Belongs to the thymidylate synthase family.

Isoforms (3)

UniProt ID	Names	Canonical?
P04818-1	1	yes
P04818-2	2, delta4
P04818-3	3, delta2+3

RefSeq proteins (3): NP_001062, NP_001341796, NP_001341797 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000398	Thymidylate_synthase	Family
IPR020940	Thymidylate_synthase_AS	Active_site
IPR023451	Thymidate_synth/dCMP_Mease_dom	Domain
IPR036926	Thymidate_synth/dCMP_Mease_sf	Homologous_superfamily
IPR045097	Thymidate_synth/dCMP_Mease	Family

Pfam: PF00303

Enzyme classification (BRENDA):

• EC 2.1.1.45 — thymidylate synthase (BRENDA: 178 organisms, 81 substrates, 400 inhibitors, 176 Km, 23 kcat entries)

Substrate kinetics (BRENDA)

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

Substrate	Km (mM)	Measurements
2’-DEOXYURIDYLATE	0.0007–0.0981	56
5,10-METHYLENETETRAHYDROFOLATE	0.0015–0.3125	25
DUMP	0.0008–0.179	22
METHYLENETETRAHYDROFOLATE	0.008–0.13	22
5-BROMO-2’-DEOXYURIDYLATE	0.0057–0.046	12
METHYLENETETRAHYDROPTEROYLGLUAMATE	0.001–0.0118	5
5-BROMO-2’-DEOXYURIDINE	0.0097–0.514	3
2’-DEOXYURIDYLATE 5’-DITHIOPHOSPHATE	0.0137–0.0155	2
2’-DEOXYURIDYLATE 5’-THIOPHOSPHATE	0.0063–0.037	2
2’-FLUORO-2’-DEOXYURIDINE 5’-PHOSPHATE	0.11–0.113	2
(-)-5,10-METHYLENE-TETRAHYDROPTEROYLGLUTAMATE	0.07	1
(6S)-TETRAHYDROPTEROYLGLUTAMATE	0.061	1
(L)-TETRAHYDROPTEROYLTRIGLUTAMATE	0.025	1
(R)-5,10-METHYLENE-5,6,7,8-TETRAHYDROFOLATE	0.3	1
(R)-5,10-METHYLENETETRAHYDROFOLATE	0.3	1

Catalyzed reactions (Rhea), 1 shown:

• dUMP + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate = 7,8-dihydrofolate + dTMP (RHEA:12104)

UniProt features (57 total): helix 14, strand 14, binding site 8, turn 6, sequence variant 4, cross-link 3, splice variant 2, initiator methionine 1, chain 1, modified residue 1, region of interest 1, compositionally biased region 1, active site 1

Structure

Experimental structures (PDB)

61 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
3ED7	X-RAY DIFFRACTION	1.56
3GH0	X-RAY DIFFRACTION	1.56
3EDW	X-RAY DIFFRACTION	1.75
3GH2	X-RAY DIFFRACTION	1.75
1YPV	X-RAY DIFFRACTION	1.8
3EAW	X-RAY DIFFRACTION	1.86
1HVY	X-RAY DIFFRACTION	1.9
5X66	X-RAY DIFFRACTION	1.99
1HW3	X-RAY DIFFRACTION	2
1HZW	X-RAY DIFFRACTION	2
3EHI	X-RAY DIFFRACTION	2
4FGT	X-RAY DIFFRACTION	2
5X5D	X-RAY DIFFRACTION	2
4KPW	X-RAY DIFFRACTION	2.03
6QXH	X-RAY DIFFRACTION	2.04
3EBU	X-RAY DIFFRACTION	2.05
1HW4	X-RAY DIFFRACTION	2.06
6QXG	X-RAY DIFFRACTION	2.08
5X4W	X-RAY DIFFRACTION	2.1
5X67	X-RAY DIFFRACTION	2.13
3EGY	X-RAY DIFFRACTION	2.18
5X4Y	X-RAY DIFFRACTION	2.2
4G2O	X-RAY DIFFRACTION	2.25
6QYQ	X-RAY DIFFRACTION	2.25
3N5E	X-RAY DIFFRACTION	2.26
4O1U	X-RAY DIFFRACTION	2.26
3N5G	X-RAY DIFFRACTION	2.27
4GD7	X-RAY DIFFRACTION	2.29
4G6W	X-RAY DIFFRACTION	2.3
4E28	X-RAY DIFFRACTION	2.3

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P04818-F1	94.05	0.90

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): 195 (nucleophile)

Ligand- & substrate-binding residues (8): 226 (in other chain); 256–258 (in other chain); 312; 50 (in other chain); 175–176; 195–196 (in other chain); 215–218 (in other chain); 218

Post-translational modifications (4): 114, 287, 292, 308

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-499943	Interconversion of nucleotide di- and triphosphates
R-HSA-69205	G1/S-Specific Transcription

MSigDB gene sets: 645 (showing top): KALMA_E2F1_TARGETS, MORF_DNMT1, WU_APOPTOSIS_BY_CDKN1A_VIA_TP53, HORIUCHI_WTAP_TARGETS_DN, KANG_DOXORUBICIN_RESISTANCE_UP, REACTOME_G1_S_SPECIFIC_TRANSCRIPTION, MORF_ESPL1, GNF2_CENPF, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, KANG_FLUOROURACIL_RESISTANCE_UP, MODULE_56, PAL_PRMT5_TARGETS_UP, KOINUMA_COLON_CANCER_MSI_UP, CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN, MORF_RRM1

GO Biological Process (9): dTMP biosynthetic process (GO:0006231), dTTP biosynthetic process (GO:0006235), negative regulation of translation (GO:0017148), methylation (GO:0032259), tetrahydrofolate interconversion (GO:0035999), DNA biosynthetic process (GO:0071897), one-carbon metabolic process (GO:0006730), nucleotide biosynthetic process (GO:0009165), tetrahydrofolate metabolic process (GO:0046653)

GO Molecular Function (8): mRNA regulatory element binding translation repressor activity (GO:0000900), thymidylate synthase activity (GO:0004799), folic acid binding (GO:0005542), sequence-specific mRNA binding (GO:1990825), dihydrofolate reductase activity (GO:0004146), methyltransferase activity (GO:0008168), transferase activity (GO:0016740), transferase activity, transferring one-carbon groups (GO:0016741)

GO Cellular Component (7): nucleus (GO:0005634), cytoplasm (GO:0005737), mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), mitochondrial matrix (GO:0005759), cytosol (GO:0005829), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Metabolism of nucleotides	1
G1/S Transition	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
pyrimidine deoxyribonucleotide biosynthetic process	2
mRNA binding	2
intracellular membrane-bounded organelle	2
cytoplasm	2
pyrimidine deoxyribonucleoside monophosphate biosynthetic process	1
dTMP metabolic process	1
deoxyribonucleoside triphosphate biosynthetic process	1
pyrimidine deoxyribonucleoside triphosphate biosynthetic process	1
dTTP metabolic process	1
translation	1
regulation of translation	1
negative regulation of gene expression	1
negative regulation of protein metabolic process	1
metabolic process	1
one-carbon metabolic process	1
tetrahydrofolate metabolic process	1
DNA metabolic process	1
nucleic acid biosynthetic process	1
small molecule metabolic process	1
nucleotide metabolic process	1
nucleoside phosphate biosynthetic process	1
folic acid-containing compound metabolic process	1
translation repressor activity	1
5,10-methylenetetrahydrofolate-dependent methyltransferase activity	1
vitamin binding	1
carboxylic acid binding	1
modified amino acid binding	1
heterocyclic compound binding	1
oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor	1
transferase activity, transferring one-carbon groups	1
catalytic activity	1
transferase activity	1
intracellular anatomical structure	1
organelle inner membrane	1
mitochondrial membrane	1
mitochondrion	1
intracellular organelle lumen	1

Protein interactions and networks

STRING

4470 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TYMS	DHFR2	Q86XF0	998
TYMS	DHFR	P00374	996
TYMS	DPYD	Q12882	978
TYMS	ENOSF1	Q7L5Y1	957
TYMS	DCTD	P32321	934
TYMS	MTHFR	P42898	916
TYMS	TYMP	P19971	910
TYMS	SHMT1	P34896	879
TYMS	TK2	O00142	876
TYMS	GART	P22102	873
TYMS	TK1	P04183	855
TYMS	SHMT2	P34897	850
TYMS	TFCP2	Q12800	845
TYMS	DTYMK	P23919	821
TYMS	UMPS	P11172	816

IntAct

39 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
TANC2	TAX1BP3	psi-mi:“MI:0914”(association)	0.690
LIMS1	TYMS	psi-mi:“MI:0914”(association)	0.530
PKIG	TYMS	psi-mi:“MI:0914”(association)	0.530
PFDN1	ARHGAP32	psi-mi:“MI:0914”(association)	0.530
VCAM1	PSMD11	psi-mi:“MI:0914”(association)	0.530
NRAS	ESYT2	psi-mi:“MI:2364”(proximity)	0.480
TYMS	EFHD2	psi-mi:“MI:0915”(physical association)	0.400
TYMS	SH3GL2	psi-mi:“MI:0915”(physical association)	0.370
Tuba3a	CCHCR1	psi-mi:“MI:0914”(association)	0.350
NS	HAUS5	psi-mi:“MI:0914”(association)	0.350
KSR1	FBLL1	psi-mi:“MI:0914”(association)	0.350
ORF70	PDHX	psi-mi:“MI:0914”(association)	0.350
RTN1	TMEM120B	psi-mi:“MI:0914”(association)	0.350
PROSER2	VWA8	psi-mi:“MI:0914”(association)	0.350
ARHGEF35	OBSL1	psi-mi:“MI:0914”(association)	0.350
CHD8	CCNE2	psi-mi:“MI:0914”(association)	0.350
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350
ATG16L1	ESYT2	psi-mi:“MI:0914”(association)	0.350
PPP4R1L	IFT56	psi-mi:“MI:0914”(association)	0.350
NAPG	NBAS	psi-mi:“MI:0914”(association)	0.350
PSD4	TYMS	psi-mi:“MI:0914”(association)	0.350
PFDN2	ARHGAP32	psi-mi:“MI:0914”(association)	0.350
SLC34A1	PSMD11	psi-mi:“MI:0914”(association)	0.350

BioGRID (119): TYMS (Affinity Capture-MS), PDCD6 (Co-fractionation), TYMS (Co-fractionation), TYMS (Co-fractionation), TYMS (Co-fractionation), TYMS (Co-fractionation), TYMS (Co-fractionation), TYMS (Co-fractionation), TYMS (Co-fractionation), TYMS (Proximity Label-MS), TYMS (Proximity Label-MS), TYMS (Proximity Label-MS), TYMS (Affinity Capture-MS), TYMS (Negative Genetic), TYMS (Affinity Capture-MS)

ESM2 similar proteins: A0B471, A2RZY1, A3MAE3, A3PGG3, A4JKF7, A5FVT7, A6M020, A9AR15, B1K259, B1YXQ0, B2IJF4, B2T319, B2TLN8, B2UIG7, B4EG09, B8GN06, B9JH03, O62584, P04818, P0DX41, P23670, P50979, P95631, Q0B5P1, Q0VM06, Q141C9, Q1BK36, Q1IZ41, Q27710, Q2L048, Q38ZU0, Q3JEI2, Q3JIC1, Q59714, Q62EK3, Q63PC7, Q67JQ1, Q7NSA6, Q89940, Q89CN4

Diamond homologs: A0JZC7, A0KG32, A1KVB3, A1SS96, A3QBR4, A4SIW7, A4WE03, A5EPD3, A5F8Y6, A5UDH0, A5UI47, A6L1Q8, A6LIC2, A6UB24, A6UYE6, A6VMA0, A6W1R4, A7HVX4, A7MR31, A7MXJ9, A8A3W0, A8AP42, A8FEB9, A8FSC3, A8H1B4, A9M657, A9MS82, A9N2L7, B0TIU4, B0UWT7, B1IU17, B7KQG2, B7LNI2, B7V2Q5, B7VJ78, B8CQK7, B8F6S2, B8I0T8, B8IF20, B9JXQ5

SIGNOR signaling

17 interactions.

A	Effect	B	Mechanism
pemetrexed	down-regulates	TYMS	“chemical inhibition”
“ICI D1694”	down-regulates	TYMS	“chemical inhibition”
TYMS	up-regulates	Purine_biosynthesis
TFDP1	“up-regulates quantity by expression”	TYMS	“transcriptional regulation”
E2F1	“up-regulates quantity by expression”	TYMS	“transcriptional regulation”
YBX1	“down-regulates quantity by repression”	TYMS	“transcriptional regulation”
“pemetrexed disodium”	“down-regulates activity”	TYMS	“chemical inhibition”
gemcitabine	“down-regulates activity”	TYMS	“chemical inhibition”
2’,2’-difluoro-2’-deoxyuridine	“down-regulates activity”	TYMS	“chemical inhibition”
pralatrexate	“down-regulates activity”	TYMS	“chemical inhibition”
capecitabine	“down-regulates activity”	TYMS	“chemical inhibition”
MYC	“up-regulates quantity by expression”	TYMS	“transcriptional regulation”
TYMS	“down-regulates quantity”	(6R)-5,10-methylenetetrahydrofolate(2-)	“chemical modification”
TYMS	“up-regulates quantity”	dihydrofolate(2-)	“chemical modification”
TYMS	“down-regulates quantity”	dUMP(2-)	“chemical modification”
TYMS	“up-regulates quantity”	dTMP(2-)	“chemical modification”
CHD8	“up-regulates quantity by expression”	TYMS	“transcriptional regulation”

Disease & clinical

Cancer significance

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	9
Likely benign	7
Benign	2

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
1693535	NM_001071.4(TYMS):c.343C>T (p.Arg115Ter)	Pathogenic
1693538	NM_001071.4(TYMS):c.534_535insTG (p.Met179Ter)	Pathogenic

SpliceAI

1230 predictions. Top by Δscore:

Variant	Effect	Δscore
18:657880:G:GT	donor_gain	1.0000
18:662317:TCAGG:T	donor_loss	1.0000
18:662318:CAGG:C	donor_loss	1.0000
18:662319:AG:A	donor_loss	1.0000
18:662320:GGT:G	donor_loss	1.0000
18:662321:GTGAG:G	donor_loss	1.0000
18:662322:T:G	donor_loss	1.0000
18:671369:C:A	acceptor_gain	1.0000
18:671370:G:A	acceptor_gain	1.0000
18:671378:A:T	acceptor_loss	1.0000
18:671379:GC:G	acceptor_gain	1.0000
18:671379:GCCA:G	acceptor_gain	1.0000
18:671448:TCAGG:T	donor_loss	1.0000
18:671449:CAGG:C	donor_loss	1.0000
18:671450:AGGTA:A	donor_loss	1.0000
18:671451:GGT:G	donor_loss	1.0000
18:671453:T:A	donor_loss	1.0000
18:674407:C:CC	acceptor_gain	1.0000
18:674408:T:G	acceptor_loss	1.0000
18:674411:C:CT	acceptor_gain	1.0000
18:674418:C:CT	acceptor_gain	1.0000
18:675315:GCTTA:G	donor_loss	1.0000
18:675316:CTTA:C	donor_loss	1.0000
18:675317:TTACC:T	donor_loss	1.0000
18:675318:TACCT:T	donor_loss	1.0000
18:675319:ACC:A	donor_loss	1.0000
18:675320:C:CA	donor_loss	1.0000
18:675399:CACC:C	acceptor_gain	1.0000
18:662142:CCAG:C	acceptor_loss	0.9900
18:662143:CAGG:C	acceptor_loss	0.9900

AlphaMissense

2047 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
18:662191:T:A	W109R	0.999
18:662191:T:C	W109R	0.999
18:662281:T:A	W139R	0.999
18:662281:T:C	W139R	0.999
18:662193:G:C	W109C	0.998
18:662193:G:T	W109C	0.998
18:669161:T:A	W182R	0.998
18:669161:T:C	W182R	0.998
18:670721:C:G	H196D	0.998
18:659665:A:T	K77I	0.997
18:659666:A:C	K77N	0.997
18:659666:A:T	K77N	0.997
18:659703:T:A	W90R	0.997
18:659703:T:C	W90R	0.997
18:670788:A:T	D218V	0.997
18:670813:C:A	N226K	0.997
18:670813:C:G	N226K	0.997
18:671413:C:G	H256D	0.997
18:662275:T:C	F137L	0.996
18:662277:C:A	F137L	0.996
18:662277:C:G	F137L	0.996
18:670720:C:G	C195W	0.996
18:670787:G:C	D218H	0.996
18:670788:A:C	D218A	0.996
18:670789:C:A	D218E	0.996
18:670789:C:G	D218E	0.996
18:670820:A:C	S229R	0.996
18:670822:C:A	S229R	0.996
18:670822:C:G	S229R	0.996
18:662273:G:A	G136D	0.995

dbSNP variants (sampled 300 via entrez): RS1000224379 (18:657639 C>A,T), RS1000910651 (18:671014 T>C), RS1000938745 (18:672802 G>A,T), RS1001036973 (18:661944 C>T), RS1001366702 (18:672556 T>A,C,G), RS1001466540 (18:658442 T>G), RS1001469524 (18:661837 T>A,C,G), RS1001622466 (18:670053 T>A), RS1001697775 (18:656343 A>G), RS1001761 (18:662103 G>A,T), RS1001773794 (18:658073 G>A,T), RS1001896935 (18:662675 C>G,T), RS1002080758 (18:657459 T>A,C), RS1002104836 (18:671695 G>A,T), RS1002139217 (18:663899 A>G)

Disease associations

OMIM: gene MIM:188350 | disease phenotypes: MIM:127550, MIM:620040

GenCC curated gene-disease

Mondo (2): dyskeratosis congenita (MONDO:0015780), dyskeratosis congenita, digenic (MONDO:0031057)

Orphanet (1): Dyskeratosis congenita (Orphanet:1775)

HPO phenotypes

84 total (30 of 84 shown, HPO-id order):

HPO	Term
HP:0000008	Abnormal morphology of female internal genitalia
HP:0000035	Abnormal testis morphology
HP:0000164	Abnormality of the dentition
HP:0000252	Microcephaly
HP:0000327	Hypoplasia of the maxilla
HP:0000365	Hearing impairment
HP:0000498	Blepharitis
HP:0000499	Abnormal eyelash morphology
HP:0000518	Cataract
HP:0000534	Abnormal eyebrow morphology
HP:0000600	Abnormality of the pharynx
HP:0000653	Sparse eyelashes
HP:0000668	Hypodontia
HP:0000670	Carious teeth
HP:0000679	Taurodontia
HP:0000704	Periodontitis
HP:0000819	Diabetes mellitus
HP:0000939	Osteoporosis
HP:0000975	Hyperhidrosis
HP:0000982	Palmoplantar keratoderma
HP:0001000	Abnormality of skin pigmentation
HP:0001018	Abnormal palmar dermatoglyphics
HP:0001034	Hypermelanotic macule
HP:0001053	Hypopigmented skin patches
HP:0001231	Abnormal fingernail morphology
HP:0001263	Global developmental delay
HP:0001394	Cirrhosis
HP:0001399	Hepatic failure
HP:0001488	Bilateral ptosis
HP:0001508	Failure to thrive

GWAS associations

10 associations (top):

Study	Trait	p-value
GCST004602_301	Mean corpuscular volume	1.000000e-09
GCST004630_223	Mean corpuscular hemoglobin	6.000000e-09
GCST004635_37	Testicular germ cell tumor	4.000000e-10
GCST008366_23	Leukocyte telomere length	1.000000e-08
GCST009733_102	Urinary metabolite levels in chronic kidney disease	4.000000e-15
GCST009856_25	Leukocyte telomere length	2.000000e-07
GCST90002390_546	Mean corpuscular hemoglobin	1.000000e-11
GCST90002392_36	Mean corpuscular volume	3.000000e-13
GCST90002396_682	Mean reticulocyte volume	8.000000e-13
GCST90002397_379	Mean spheric corpuscular volume	4.000000e-14

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004527	mean corpuscular hemoglobin
EFO:0005116	urinary metabolite measurement
EFO:0010701	mean reticulocyte volume

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D019871	Dyskeratosis Congenita	C15.378.190.223.500.750; C16.131.831.150; C16.320.322.108; C16.320.850.235; C17.800.804.150; C17.800.827.235

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (3): CHEMBL1952 (SINGLE PROTEIN), CHEMBL3885527 (PROTEIN FAMILY), CHEMBL3885528 (PROTEIN FAMILY)

Molecules with ChEMBL bioactivity

9 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 1,165,436 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

Molecule	Name	Phase	Patents
CHEMBL1622	FOLIC ACID	4	525,158
CHEMBL225071	RALTITREXED	4	96,748
CHEMBL225072	PEMETREXED	4	55,761
CHEMBL2360464	PEMETREXED DISODIUM	4	21,546
CHEMBL34259	METHOTREXATE	4	398,396
CHEMBL63857	PHENOLPHTHALEIN	4	57,577
CHEMBL320775	NOLATREXED	3	9,952
CHEMBL169896	OSI-7904	2	243
CHEMBL9440	METESIND	2	55

Clinical evidence (CIViC)

Drug × variant × indication: 8 predictive associations from 10 curated evidence items.

Variant	Therapy	Indication	Effect	Level	CIViC
TYMS Underexpression	Pemetrexed	Lung Non-small Cell Carcinoma	Sensitivity/Response	CIViC B	EID907
TYMS Amplification	5-Fluorouracil/Salicylic Acid Topical Solution	Colorectal Cancer	Resistance	CIViC B	EID12097 +1
TYMS Overexpression	Pemetrexed	Lung Non-small Cell Carcinoma	Resistance	CIViC B	EID832 +1
TYMS 3TRP/3TRP genotype	Fluorouracil + Irinotecan	Colorectal Cancer	Resistance	CIViC B	EID678
TYMS Amplification	Pemetrexed	Lung Adenocarcinoma	Resistance	CIViC B	EID903
TYMS Overexpression	Raltitrexed	Gastric Adenocarcinoma	Resistance	CIViC B	EID929
TYMS RS34743033	Methotrexate	Cancer	Adverse Response	CIViC B	EID1843
TYMS Underexpression	Pemetrexed	Prostate Cancer	Sensitivity/Response	CIViC C	EID908

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

PharmGKB clinical annotations

18 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs11280056	Toxicity	3	methotrexate	Acute lymphoblastic leukemia;Gastrointestinal toxicity;Mucositis;Neutropenia
rs11280056	Efficacy	3	methotrexate	Acute lymphoblastic leukemia;Rheumatoid arthritis
rs11280056	Efficacy	3	fluorouracil	Colorectal Neoplasms
rs11280056	Efficacy	3	pemetrexed	Mesothelioma
rs11280056	Toxicity	3	fluorouracil;FOLFOX	Neoplasms
rs11280056	Toxicity	4	methotrexate	Drug Toxicity;Hematopoietic stem cell transplantation;Psoriasis;Rheumatoid arthritis;Toxic liver disease
rs183205964	Toxicity	3	capecitabine;fluorouracil;tegafur	Neoplasms
rs2847153	Efficacy	3	fluorouracil	Pancreatic Neoplasms
rs2853539	Efficacy	3	methotrexate	Rheumatoid arthritis
rs2853741	Toxicity	3	capecitabine	Diarrhea;Neoplasms
rs45445694	Efficacy	3	methotrexate	Rheumatoid arthritis
rs45445694	Metabolism/PK	4	methotrexate	Acute lymphoblastic leukemia
rs45445694	Efficacy	3	fluorouracil;FOLFIRI;FOLFOX	Overall survival;Progression-free survival
rs45445694	Toxicity	3	fluorouracil	Drug Toxicity
rs45445694	Toxicity	3	irinotecan;raltitrexed	Colorectal Neoplasms
rs45445694	Efficacy	3	methotrexate	Acute lymphoblastic leukemia;Neoplasms
rs45445694	Toxicity	3	methotrexate	Acute lymphoblastic leukemia;Non-Hodgkin Lymphoma
rs699517	Toxicity	3	capecitabine	Asthenia;Nausea;Neoplasms;Vomiting

PharmGKB variants

11 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs2847153	TYMS	3	2.50	1	fluorouracil
rs2853539	C18orf56, TYMS	3	3.25	1	methotrexate
rs45445694	C18orf56, TYMS	3	7.50	7	irinotecan;raltitrexed;methotrexate;fluorouracil;FOLFIRI;FOLFOX;fluorouracil
rs183205964	TYMS	3	3.00	1	capecitabine;fluorouracil;tegafur
rs2853542	TYMS		0.00	0
rs699517	ENOSF1, TYMS	3	5.50	1	capecitabine
rs2853741	TYMS	3	3.25	1	capecitabine
rs2244500	TYMS		0.00	0
rs11280056	ENOSF1, TYMS	3	3.50	6	methotrexate;fluorouracil;fluorouracil;FOLFOX;pemetrexed
rs3786362	TYMS		0.00	0
rs2790	ENOSF1, TYMS		0.00	0

GtoPdb / IUPHAR curated pharmacology

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

Target class: enzyme — 2.1.1.- Methyltransferases

Most potent curated ligand interactions (4 total), top 4:

Ligand	Action	Affinity	Parameter
plevitrexed	Inhibition	9.36	pKi
ONX-0801	Inhibition	8.92	pKi
pemetrexed	Inhibition	6.96	pKi
raltitrexed	Inhibition	6.54	pIC50

Binding affinities (BindingDB)

12 measured of 35 human assays (89 total across all organisms); most potent 12 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value	Patent
4-(3-bromo-4-hydroxyphenyl)-4-(4-hydroxyphenyl)-3-oxatricyclo[7.3.1.0^{5,13}]trideca-1(12),5,7,9(13),10-pentaen-2-one	KI	3400 nM
3,3-bis(4-hydroxy-3-iodophenyl)-4-oxatricyclo[7.4.0.0^{2,6}]trideca-1(9),2(6),7,10,12-pentaen-5-one	KI	3900 nM
4,4-bis(3,5-dibromo-4-hydroxyphenyl)-3-oxatricyclo[7.3.1.0^{5,13}]trideca-1(12),5,7,9(13),10-pentaen-2-one	KI	9500 nM
4,4-bis(3-bromo-4-hydroxyphenyl)-3-oxatricyclo[7.3.1.0^{5,13}]trideca-1(12),5,7,9(13),10-pentaen-2-one	KI	15000 nM
5-(phenylthio)-9H-pyrimido[4,5-b]indole-2,4-diamine	IC50	15100 nM	US-9422297: Tricyclic compounds having cytostatic and/or cytotoxic activity and methods of use thereof
4,4-bis(3,5-dichloro-4-hydroxyphenyl)-3-oxatricyclo[7.3.1.0^{5,13}]trideca-1(12),5,7,9(13),10-pentaen-2-one	KI	28000 nM
5,5-bis(4-hydroxyphenyl)-4-oxatricyclo[7.4.0.0^{2,6}]trideca-1(9),2(6),7,10,12-pentaen-3-one	KI	35000 nM
5,5-bis(3-chloro-4-hydroxyphenyl)-4-oxatricyclo[7.4.0.0^{2,6}]trideca-1(9),2(6),7,10,12-pentaen-3-one	KI	35000 nM
4,4-bis(4-hydroxy-3-iodophenyl)-3-oxatricyclo[7.3.1.0^{5,13}]trideca-1(12),5,7,9(13),10-pentaen-2-one	KI	94000 nM
5,5-bis(3-fluoro-4-hydroxyphenyl)-4-oxatricyclo[7.4.0.0^{2,6}]trideca-1(9),2(6),7,10,12-pentaen-3-one	KI	109000 nM
3,3-bis(4-hydroxyphenyl)-4-oxatricyclo[7.4.0.0^{2,6}]trideca-1(9),2(6),7,10,12-pentaen-5-one	KI	110000 nM
2-[(4-{(2,4-diaminopteridin-6-yl)methylamino}phenyl)formamido]pentanedioic acid	KI	137000 nM

ChEMBL bioactivities

717 potent at pChembl≥5 of 882 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
10.39	Ki	0.041	nM	CHEMBL290277
10.38	Ki	0.042	nM	CHEMBL406575
10.14	Ki	0.072	nM	CHEMBL295708
10.11	IC50	0.078	nM	CHEMBL4177183
10.05	Ki	0.09	nM	OSI-7904
10.05	Ki	0.09	nM	CHEMBL355323
9.91	Ki	0.124	nM	CHEMBL166027
9.85	IC50	0.14	nM	CHEMBL4162649
9.65	Ki	0.224	nM	CHEMBL295681
9.36	Ki	0.44	nM	CHEMBL168907
8.96	Ki	1.1	nM	CHEMBL169506
8.92	IC50	1.2	nM	CHEMBL1253498
8.92	Ki	1.2	nM	CHEMBL355662
8.89	Ki	1.3	nM	PEMETREXED
8.88	Ki	1.31	nM	CHEMBL166369
8.82	Ki	1.5	nM	CHEMBL179448
8.70	Ki	2	nM	CHEMBL9671
8.70	Ki	2	nM	METESIND
8.62	IC50	2.4	nM	CHEMBL4531593
8.60	Ki	2.5	nM	CHEMBL325972
8.60	Ki	2.5	nM	CHEMBL355616
8.52	IC50	3	nM	CHEMBL321678
8.52	IC50	3	nM	CHEMBL5267424
8.52	IC50	3	nM	CHEMBL111859
8.52	IC50	3	nM	CHEMBL113019
8.52	IC50	3	nM	CHEMBL109881
8.52	IC50	3	nM	CHEMBL320036
8.52	IC50	3	nM	CHEMBL264198
8.52	IC50	3	nM	CHEMBL5289121
8.52	IC50	3	nM	CHEMBL5289689
8.52	IC50	3	nM	CHEMBL5283610
8.52	IC50	3	nM	CHEMBL5287291
8.52	IC50	3	nM	CHEMBL5288172
8.52	IC50	3	nM	CHEMBL5268759
8.52	IC50	3	nM	CHEMBL5286548
8.52	IC50	3	nM	CHEMBL5282201
8.52	IC50	3	nM	CHEMBL5266971
8.52	IC50	3	nM	CHEMBL5271165
8.52	IC50	3	nM	CHEMBL5273148
8.48	Ki	3.3	nM	CHEMBL3099582
8.40	Ki	4	nM	CHEMBL55263
8.40	Ki	4	nM	CHEMBL167164
8.39	Ki	4.1	nM	CHEMBL362606
8.35	Ki	4.5	nM	CHEMBL422395
8.33	IC50	4.7	nM	CHEMBL1160192
8.32	Ki	4.77	nM	CHEMBL253954
8.26	Ki	5.5	nM	CHEMBL324739
8.26	IC50	5.5	nM	CHEMBL1160188
8.22	Ki	6	nM	CHEMBL56523
8.22	Ki	6	nM	CHEMBL168524

PubChem BioAssay actives

771 with measured affinity, of 1796 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.

Compound	Assay	Type	Value	Unit
2-[[4-[[4-[[4-[[4-[(2-amino-4-oxo-3H-quinazolin-6-yl)methyl-prop-2-ynylamino]benzoyl]amino]-4-carboxybutanoyl]amino]-4-carboxybutanoyl]amino]-4-carboxybutanoyl]amino]pentanedioic acid	212471: Compound was tested for inhibition of human (WI-L2) thymidylate synthase	ki	<0.0001	uM
2-[[4-[[4-[[4-[[4-[[4-[(2-amino-4-oxo-3H-quinazolin-6-yl)methyl-prop-2-ynylamino]benzoyl]amino]-4-carboxybutanoyl]amino]-4-carboxybutanoyl]amino]-4-carboxybutanoyl]amino]-4-carboxybutanoyl]amino]pentanedioic acid	212471: Compound was tested for inhibition of human (WI-L2) thymidylate synthase	ki	<0.0001	uM
(2S)-2-[6-[(3-methyl-1-oxo-2H-benzo[f]quinazolin-9-yl)methylamino]-3-oxo-1H-isoindol-2-yl]pentanedioic acid	212325: The compound was tested for inhibitory activity against thymidylate synthase (purified recombinant human gene) from Escherichia coli	ki	0.0001	uM
(2S)-2-[[2-fluoro-4-[(3-methyl-1-oxo-2H-benzo[f]quinazolin-9-yl)methylamino]benzoyl]amino]pentanedioic acid	212325: The compound was tested for inhibitory activity against thymidylate synthase (purified recombinant human gene) from Escherichia coli	ki	0.0001	uM
(2R)-2-[[4-[(2-amino-6-methyl-4-oxo-3H-quinazolin-5-yl)sulfanyl]benzoyl]amino]pentanedioic acid	221979: Compound was tested for TS activity against human Thymidylate synthase by tight binding kinetics	ki	0.0001	uM
2-[[4-[[4-[[4-[(2-amino-4-oxo-3H-quinazolin-6-yl)methyl-prop-2-ynylamino]benzoyl]amino]-4-carboxybutanoyl]amino]-4-carboxybutanoyl]amino]pentanedioic acid	212471: Compound was tested for inhibition of human (WI-L2) thymidylate synthase	ki	0.0001	uM
(2S)-2-[6-[[2-(2-amino-4-oxo-3,7-dihydropyrrolo[2,3-d]pyrimidin-6-yl)acetyl]amino]hexanoylamino]pentanedioic acid	1501141: Inhibition of TS/AICARFTase/GARFTase in human KB cells assessed as reduction in cell proliferation in folate free medium after 72 hrs in presence of leucovorin by MTT assay	ic50	0.0001	uM
(2S)-2-[[2-[[2-(2-amino-4-oxo-3,7-dihydropyrrolo[2,3-d]pyrimidin-6-yl)acetyl]amino]acetyl]amino]pentanedioic acid	1501141: Inhibition of TS/AICARFTase/GARFTase in human KB cells assessed as reduction in cell proliferation in folate free medium after 72 hrs in presence of leucovorin by MTT assay	ic50	0.0001	uM
2-[[4-[[4-[(2-amino-4-oxo-3H-quinazolin-6-yl)methyl-prop-2-ynylamino]benzoyl]amino]-4-carboxybutanoyl]amino]pentanedioic acid	212471: Compound was tested for inhibition of human (WI-L2) thymidylate synthase	ki	0.0002	uM
(2S)-2-[[4-[(3-methyl-1-oxo-2H-benzo[f]quinazolin-9-yl)methylamino]benzoyl]amino]pentanedioic acid	212326: The compound was tested for inhibitory activity against thymidylate synthase (purified recombinant human gene) from Escherichia coli.	ki	0.0004	uM
(2S)-2-[[5-[(3-methyl-1-oxo-2H-benzo[f]quinazolin-9-yl)methylamino]thiophene-2-carbonyl]amino]pentanedioic acid	212325: The compound was tested for inhibitory activity against thymidylate synthase (purified recombinant human gene) from Escherichia coli	ki	0.0011	uM
(2S)-2-[[4-[(3-amino-1-oxo-2H-benzo[f]quinazolin-9-yl)methylamino]benzoyl]amino]pentanedioic acid	212326: The compound was tested for inhibitory activity against thymidylate synthase (purified recombinant human gene) from Escherichia coli.	ki	0.0012	uM
(2R)-2-[[(4S)-4-carboxy-4-[[4-[[2-(hydroxymethyl)-4-oxo-3,6,7,8-tetrahydrocyclopenta[g]quinazolin-6-yl]-prop-2-ynylamino]benzoyl]amino]butanoyl]amino]pentanedioic acid	513674: Inhibition of thymine synthase	ic50	0.0012	uM
Pemetrexed	1894188: Inhibition of thymidylate synthase (unknown origin) assessed as inhibition constant	ki	0.0013	uM
(2R)-2-[[4-[(2,6-dimethyl-4-oxo-3H-quinazolin-5-yl)sulfanyl]benzoyl]amino]pentanedioic acid	221979: Compound was tested for TS activity against human Thymidylate synthase by tight binding kinetics	ki	0.0013	uM
(2S)-2-(benzo[g][1,2,3]benzoxadiazol-5-ylsulfonylamino)-3-[4-[5-(dimethylamino)naphthalen-1-yl]sulfonyloxyphenyl]propanoic acid	238383: Inhibitory constant against human thymidylate synthase	ki	0.0015	uM
N,5-dimethyl-2-methylimino-N-[(4-morpholin-4-ylsulfonylphenyl)methyl]-1H-benzo[cd]indol-6-amine	212333: Compound was evaluated for the inhibitory constant of human thymidylate synthase	ki	0.0020	uM
6-N-methyl-6-N-[(4-morpholin-4-ylsulfonylphenyl)methyl]benzo[cd]indole-2,6-diamine	212333: Compound was evaluated for the inhibitory constant of human thymidylate synthase	ki	0.0020	uM
(2S)-4-[1-(carboxymethyl)tetrazol-5-yl]-2-[[4-[(2,7-dimethyl-4-oxo-3H-quinazolin-6-yl)methyl-ethynylamino]-2-fluorobenzoyl]amino]butanoic acid	1567370: Inhibition of thymidylate synthase (unknown origin)	ic50	0.0024	uM
(2S)-2-[6-[methyl-[(3-methyl-1-oxo-2H-benzo[f]quinazolin-9-yl)methyl]amino]-3-oxo-1H-isoindol-2-yl]pentanedioic acid	212325: The compound was tested for inhibitory activity against thymidylate synthase (purified recombinant human gene) from Escherichia coli	ki	0.0025	uM
(2S)-2-[[4-[(3-amino-1-oxo-5,6-dihydro-2H-benzo[f]quinazolin-9-yl)sulfonylamino]benzoyl]amino]pentanedioic acid	212336: Inhibition of purified human thymidylate synthase isolated from an Escherichia coli harboring thy A gene cloned from SV40 transformed human fibroblast cells	ki	0.0025	uM
methyl 3-[(1S)-1-[[4-[(2-amino-6-methyl-4-oxo-3H-quinazolin-5-yl)sulfanyl]benzoyl]amino]-2-methoxy-2-oxoethyl]benzoate	1959939: Inhibition of human TS	ic50	0.0030	uM
methyl (2S)-2-[[4-[(2-amino-6-methyl-4-oxo-3H-quinazolin-5-yl)sulfanyl]benzoyl]amino]-2-phenylacetate	1959939: Inhibition of human TS	ic50	0.0030	uM
(2S)-2-[[4-[(2-amino-6-methyl-4-oxo-3H-quinazolin-5-yl)sulfanyl]benzoyl]amino]-2-phenylacetic acid	1959939: Inhibition of human TS	ic50	0.0030	uM
(2S)-2-[[4-[(2-amino-6-methyl-4-oxo-3H-quinazolin-5-yl)sulfanyl]benzoyl]amino]-2-(3-hydroxyphenyl)acetic acid	1959939: Inhibition of human TS	ic50	0.0030	uM
3-[(S)-[[4-[(2-amino-6-methyl-4-oxo-3H-quinazolin-5-yl)sulfanyl]benzoyl]amino]-carboxymethyl]benzoic acid	1959939: Inhibition of human TS	ic50	0.0030	uM
methyl (2S)-2-[[4-[(2-amino-6-methyl-4-oxo-3H-quinazolin-5-yl)sulfanyl]benzoyl]amino]-2-(3-hydroxyphenyl)acetate	1959939: Inhibition of human TS	ic50	0.0030	uM
methyl (2S)-2-[[4-[(2-amino-6-methyl-4-oxo-3H-quinazolin-5-yl)sulfanyl]benzoyl]amino]-3-(4-hydroxyphenyl)propanoate	1959939: Inhibition of human TS	ic50	0.0030	uM
methyl 3-[[4-[(2-amino-6-methyl-4-oxo-3H-quinazolin-5-yl)sulfanyl]benzoyl]amino]benzoate	1959939: Inhibition of human TS	ic50	0.0030	uM
methyl (2S)-2-[[4-[(2-amino-6-methyl-4-oxo-3H-quinazolin-5-yl)sulfanyl]benzoyl]amino]-3-phenylpropanoate	1959939: Inhibition of human TS	ic50	0.0030	uM
methyl (2S)-2-[[4-[(2-amino-6-methyl-4-oxo-3H-quinazolin-5-yl)sulfanyl]benzoyl]amino]-3-(3,4-dihydroxyphenyl)propanoate	1959939: Inhibition of human TS	ic50	0.0030	uM
methyl (2S)-2-[[5-[(2-amino-6-methyl-4-oxo-3H-quinazolin-5-yl)sulfanyl]thiophene-2-carbonyl]amino]-2-phenylacetate	1959939: Inhibition of human TS	ic50	0.0030	uM
3-[[4-[(2-amino-6-methyl-4-oxo-3H-quinazolin-5-yl)sulfanyl]benzoyl]amino]benzoic acid	1959939: Inhibition of human TS	ic50	0.0030	uM
(2S)-2-[[4-[(2-amino-6-methyl-4-oxo-3H-quinazolin-5-yl)sulfanyl]benzoyl]amino]-3-phenylpropanoic acid	1959939: Inhibition of human TS	ic50	0.0030	uM
4-[(2-amino-6-methyl-4-oxo-3H-quinazolin-5-yl)sulfanyl]-N-[(1S)-2-hydroxy-1-phenylethyl]benzamide	1959939: Inhibition of human TS	ic50	0.0030	uM
4-[(2-amino-6-methyl-4-oxo-3H-quinazolin-5-yl)sulfanyl]-N-[(1R)-1-phenylethyl]benzamide	1959939: Inhibition of human TS	ic50	0.0030	uM
methyl (2S)-2-[[4-[(2-amino-6-methyl-4-oxo-3H-quinazolin-5-yl)sulfanyl]benzoyl]amino]-3-(1H-indol-3-yl)propanoate	1959939: Inhibition of human TS	ic50	0.0030	uM
methyl (2R)-2-[[4-[(2-amino-6-methyl-4-oxo-3H-quinazolin-5-yl)sulfanyl]benzoyl]amino]-2-phenylacetate	1959939: Inhibition of human TS	ic50	0.0030	uM
methyl (2S)-2-[[4-[(2-amino-6-methyl-4-oxo-3H-quinazolin-5-yl)sulfanyl]benzoyl]amino]-3-(4-aminophenyl)propanoate	1959939: Inhibition of human TS	ic50	0.0030	uM
2-amino-5-naphthalen-2-ylsulfanyl-3,9-dihydropyrimido[4,5-b]indol-4-one	1059662: Inhibition of human TS using dUMP and methylene-THF as substrate by kaleidagraph analysis	ki	0.0033	uM
6-N,5-dimethyl-6-N-[(2-methyl-4-pyridinyl)methyl]benzo[cd]indole-2,6-diamine	212458: Inhibitory effect against recombinant human thymidylate synthase	ki	0.0040	uM
(2S)-2-[6-[(3-methyl-1-oxo-2H-benzo[f]quinazolin-9-yl)methylamino]-3-oxo-1,2-benzothiazol-2-yl]pentanedioic acid	212325: The compound was tested for inhibitory activity against thymidylate synthase (purified recombinant human gene) from Escherichia coli	ki	0.0040	uM
(2S)-3-[4-[5-(dimethylamino)naphthalen-1-yl]sulfonyloxyphenyl]-2-[(6-nitronaphthalen-1-yl)sulfonylamino]propanoic acid	238383: Inhibitory constant against human thymidylate synthase	ki	0.0041	uM
2-[[4-[(2-amino-4-oxo-3H-quinazolin-6-yl)methyl-prop-2-ynylamino]benzoyl]amino]pentanedioic acid	212331: Binding affinity against human thymidylate synthase	ki	0.0045	uM
2-[[4-[[4-[[2-[[4-[(2-amino-4-oxo-3H-quinazolin-6-yl)methyl-ethynylamino]benzoyl]amino]-4-carboxybutanoyl]amino]-4-carboxybutanoyl]amino]-4-carboxybutanoyl]amino]pentanedioic acid	211796: Inhibitory activity against thymidylate synthase of Streptococcus faecium	ic50	0.0047	uM
[(2R,3R,4S,5R)-4-fluoro-5-(5-fluoro-2,4-dioxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methyl dihydrogen phosphate	328153: Binding affinity to human recombinant thymidylate synthase	ki	0.0048	uM
2-[[4-[[4-[[4-[(2-amino-4-oxo-3H-quinazolin-6-yl)methyl-ethynylamino]benzoyl]amino]-4-carboxybutanoyl]amino]-4-carboxybutanoyl]amino]pentanedioic acid	211796: Inhibitory activity against thymidylate synthase of Streptococcus faecium	ic50	0.0055	uM
(2S)-2-[[4-[(3-methyl-1-oxo-2H-benzo[f]quinazolin-9-yl)sulfonylamino]benzoyl]amino]pentanedioic acid	212325: The compound was tested for inhibitory activity against thymidylate synthase (purified recombinant human gene) from Escherichia coli	ki	0.0055	uM
6-N,5-dimethyl-6-N-(pyridin-4-ylmethyl)benzo[cd]indole-2,6-diamine	212458: Inhibitory effect against recombinant human thymidylate synthase	ki	0.0060	uM
5-[(4-morpholin-4-ylsulfonylphenyl)methyl]-1,6,7,8-tetrahydroimidazo[4,5-g]quinolin-2-amine	212334: Inhibition of human Thymidylate synthase (TS)	ki	0.0060	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Fluorouracil	decreases expression, increases expression, increases activity, affects expression, increases response to substance (+7 more)	75
Cisplatin	decreases expression, increases activity, increases expression, increases stability, affects response to substance (+8 more)	8
Methotrexate	affects response to substance, decreases response to substance, increases response to substance, decreases expression, increases expression	8
Arsenic Trioxide	decreases expression, increases expression, decreases response to substance, affects activity, affects expression (+1 more)	7
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression, affects binding (+1 more)	5
Oxaliplatin	affects cotreatment, affects response to substance, increases response to substance, decreases expression	5
Leucovorin	affects cotreatment, decreases expression, increases response to substance, affects response to substance	5
bisphenol A	affects expression, decreases expression, increases expression	4
raltitrexed	decreases activity, affects response to substance, decreases reaction, increases expression	4
benzyloxycarbonylleucyl-leucyl-leucine aldehyde	decreases reaction, affects cotreatment, decreases stability, decreases expression	4
(+)-JQ1 compound	affects binding, decreases expression	4
Benzo(a)pyrene	decreases expression, increases expression	4
Estradiol	decreases reaction, increases expression	4
Floxuridine	affects response to substance, decreases response to substance, increases response to substance	4
Folic Acid	affects expression, decreases activity, increases expression	4
Cyclosporine	affects cotreatment, decreases expression	4
Paclitaxel	affects cotreatment, decreases expression, decreases reaction, affects expression, increases expression (+1 more)	4
Pemetrexed	decreases activity, affects response to substance, decreases reaction, increases expression	3
Capecitabine	affects cotreatment, affects response to substance, decreases response to substance, affects expression	3
Rotenone	decreases expression	3
Tetrachlorodibenzodioxin	decreases reaction, increases expression, decreases expression	3
Tretinoin	decreases expression	3
Aflatoxin B1	affects expression, increases expression	3
Particulate Matter	decreases expression, increases abundance, affects cotreatment, decreases abundance, increases expression	3
methylselenic acid	decreases expression, affects expression	2
trichostatin A	decreases expression, decreases reaction, increases response to substance, increases degradation	2
cobaltous chloride	affects cotreatment, increases expression, decreases expression	2
doxifluridine	affects expression, affects cotreatment, decreases response to substance	2
2,3-dimethoxy-1,4-naphthoquinone	increases expression	2
palbociclib	decreases expression	2

ChEMBL screening assays

376 unique, capped per target: 373 binding, 2 admet, 1 functional

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL1029822	Binding	Inhibition of human thymidylate synthase	Novel non-active site inhibitor of Cryptosporidium hominis TS-DHFR identified by a virtual screen. — Bioorg Med Chem Lett
CHEMBL4409186	ADMET	Inhibition of recombinant human His6-tagged TS using dUMP and 5,10-methylenetetrahydrofolate as substrate by spectrometry	Structure activity relationship towards design of cryptosporidium specific thymidylate synthase inhibitors. — Eur J Med Chem
CHEMBL821247	Functional	Compound was evaluated for time-dependent loss of activity with use of 15 nM of dTMP synthetase enzyme from chick embryo in the presence of 0.15 nM of CH2-H4 folate at about 20 seconds	Interaction of N4-hydroxy-2’-deoxycytidylic acid with thymidylate synthetase. — J Med Chem

Cellosaurus cell lines

11 cell lines: 10 cancer cell line, 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_4J75	SKG-I/TS	Cancer cell line	Female
CVCL_4J77	SKG-II/TS	Cancer cell line	Female
CVCL_B7N5	A549/TS1	Cancer cell line	Male
CVCL_B7N6	A549/TS2	Cancer cell line	Male
CVCL_B7N7	H1299/TS1	Cancer cell line	Male
CVCL_B7N8	H1299/TS2	Cancer cell line	Male
CVCL_B7N9	PC9/TS1	Cancer cell line	Male
CVCL_B7NA	PC9/TS2	Cancer cell line	Male
CVCL_D2DJ	Abcam HCT 116 TYMS KO	Cancer cell line	Male
CVCL_D2PD	Abcam THP-1 TYMS KO	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00004787	PHASE2	COMPLETED	Phase II Pilot Study of Granulocyte Colony-Stimulating Factor for Inherited Bone Marrow Failure Syndromes
NCT01659606	PHASE2	ACTIVE_NOT_RECRUITING	Radiation- and Alkylator-free Bone Marrow Transplantation Regimen for Patients With Dyskeratosis Congenita
NCT03579875	PHASE2	RECRUITING	Alpha/Beta TCD HCT in Patients With Inherited BMF Disorders
NCT04232085	PHASE2	RECRUITING	Regenerative Medicine to Restore Hematopoiesis and Immune Function in Immunodeficiencies and Inherited Bone Marrow Failures
NCT04638517	PHASE2	TERMINATED	The TELO-SCOPE Study: Attenuating Telomere Attrition With Danazol. Is There Scope to Dramatically Improve Health Outcomes for Adults and Children With Pulmonary Fibrosis
NCT01917708	PHASE1	COMPLETED	Bone Marrow Transplant With Abatacept for Non-Malignant Diseases
NCT06477614	PHASE1	RECRUITING	Anti-cancer DC Cell Vaccination to Treat Solid Tumors
NCT06817590	PHASE1	RECRUITING	Nucleoside Therapy in Patients With Telomere Biology Disorders
NCT00455312	PHASE2/PHASE3	COMPLETED	Stem Cell Transplant (SCT) for Dyskeratosis Congenita or SAA
NCT01001598	PHASE1/PHASE2	TERMINATED	Safety and Efficacy Trial of Danazol in Patients With Fanconi Anemia or Dyskeratosis Congenita
NCT00027274	Not specified	RECRUITING	Cancer in Inherited Bone Marrow Failure Syndromes
NCT00499070	Not specified	COMPLETED	Assessing Immune Function in Young Patients With Cytopenia That Did Not Respond to Treatment
NCT01319851	Not specified	TERMINATED	Alefacept and Allogeneic Hematopoietic Stem Cell Transplantation
NCT02162420	Not specified	COMPLETED	Hematopoietic Stem Cell Transplant for Dyskeratosis Congenita or Severe Aplastic Anemia
NCT02720679	Not specified	RECRUITING	Investigation of the Genetics of Hematologic Diseases
NCT03050268	Not specified	RECRUITING	Familial Investigations of Childhood Cancer Predisposition
NCT04959188	Not specified	COMPLETED	Needs Assessment for Individuals and Families Affected by Dyskeratosis Congenita (DC) and Related Telomere Biology Disorders (TBD)
NCT06731036	Not specified	AVAILABLE	Expanded Access to CD34+ Selection Utilizing Miltenyi CliniMACS Prodigy® for Patients Receiving Peripheral Blood Stem Cell Transplantations and Stem Cell Boosts