KpKP13 Protein target profile

Thymidylate synthase

Accession: KP13_02286

Gene: thyA AHE42858.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GX29
Length 264
Pocket druggability (P2Rank · AlphaFold DB model) 0.956
Direct ligand evidence 0 183 total records
Functional annotation 1 EC 6 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
Hit
Human identity (%)
50.709 Lower values reduce human off-target concern.
Human E-value
8.93e-96
Gut microbiome similarity
23.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
93.939 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
98.17 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.956
Structure A0A0H3GX29
Pocket Pocket 1
Druggability (FPocket) 0.307
Structure A0A0H3GX29
Pocket Pocket 13
ColabFold model
P2Rank 0.965 · Pocket 1
FPocket 0.721 · Pocket 9
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 1091 / 4744 genomes with a hit
Prevalence 23.0%

Sequence

Primary amino-acid sequence viewer.

MKQYLDLMQKVLTEGTPKNDRTGTGTISIFGHQMRFNLQEGFPLVTTKRCHLRSIIHELLWFLQGDTNIAYLHENNVTIWDEWADENGDLGPVYGKQWRSWPAPDGRHIDQISTVMNQLKNDPDSRRIIVSAWNVGELDKMALAPCHAFFQFYVADGKLSCQLYQRSCDVFLGLPFNIASYALLVHMVAQQCDLQVGDFVWTGGDTHLYSNHLEQTNLQLSREPRPLPKLVIKRKPASIFDYRFEDFEIEGYDPHPGIKAPVAI

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0016741 Catalysis of the transfer of a one-carbon group from one compound (donor) to another (acceptor).
  • GO:0004799 Catalysis of the reaction: 5,10-methylenetetrahydrofolate + dUMP = 7,8-dihydrofolate + thymidylate.
  • GO:0006231 The chemical reactions and pathways resulting in the formation of dTMP, deoxyribosylthymine monophosphate (2'-deoxyribosylthymine 5'-phosphate).
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0006235 The chemical reactions and pathways resulting in the formation of dTTP, deoxyribosylthymine triphosphate.
  • GO:0032259 The process in which a methyl group is covalently attached to a molecule.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
1 264 Hamap MF_00008 Thymidylate synthase [thyA].
1 264 InterPro IPR000398 Thymidylate synthase
1 264 FunFam G3DSA:3.30.572.10:FF:000001 Thymidylate synthase
84 264 NCBIfam TIGR03284 thymidylate synthase
84 264 InterPro IPR000398 Thymidylate synthase
2 85 NCBIfam TIGR03284 thymidylate synthase
2 85 InterPro IPR000398 Thymidylate synthase
126 154 ProSitePatterns PS00091 Thymidylate synthase active site.
126 154 InterPro IPR020940 Thymidylate synthase, active site
2 264 Pfam PF00303 Thymidylate synthase
2 264 InterPro IPR023451 Thymidylate synthase/dCMP hydroxymethylase domain
3 215 CDD cd00351 TS_Pyrimidine_HMase
3 215 InterPro IPR023451 Thymidylate synthase/dCMP hydroxymethylase domain
115 134 PRINTS PR00108 Thymidylate synthase family signature
115 134 InterPro IPR000398 Thymidylate synthase
197 214 PRINTS PR00108 Thymidylate synthase family signature
197 214 InterPro IPR000398 Thymidylate synthase
159 185 PRINTS PR00108 Thymidylate synthase family signature
159 185 InterPro IPR000398 Thymidylate synthase
141 156 PRINTS PR00108 Thymidylate synthase family signature
141 156 InterPro IPR000398 Thymidylate synthase
42 63 PRINTS PR00108 Thymidylate synthase family signature
42 63 InterPro IPR000398 Thymidylate synthase
2 264 PANTHER PTHR11548 THYMIDYLATE SYNTHASE 1
2 264 InterPro IPR045097 Thymidylate synthase/dCMP hydroxymethylase
1 264 SUPERFAMILY SSF55831 Thymidylate synthase/dCMP hydroxymethylase
1 264 InterPro IPR036926 Thymidylate synthase/dCMP hydroxymethylase superfamily
1 264 Gene3D G3DSA:3.30.572.10 Thymidylate synthase/dCMP hydroxymethylase domain

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.956
Likely same site as FPocket 13 1.4 Å 28 shared residues 88% of smaller site
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.045
Show in viewer
Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #13
0.307 Unusual size
Likely same site as P2Rank 1 1.4 Å 28 shared residues 88% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:146-146
UniProt: Binding site:126-127
UniProt: Binding site:166-169 in other chain
UniProt: Binding site:169-169
UniProt: Binding site:177-177 in other chain
UniProt: Binding site:207-209 in other chain
UniProt: Binding site:21-21 in other chain
UniProt: Binding site:263-263
UniProt: Binding site:51-51
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GX29
AlphaFold DB full sequence Viewing
ColabFold KP13_02286
ColabFold full sequence Loaded

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

183 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 133 records from similar proteins
Structural ligands 33 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
14C PDB via homolog 272.7 Da · LogP 2.84 · TPSA 50.3 Open detail RCSB PDB
1JY PDB via homolog Detail RCSB PDB
2BR PDB via homolog Detail RCSB PDB
C2F PDB via homolog Detail RCSB PDB
CF9 PDB via homolog Detail RCSB PDB

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
14C RCSB PDB P00469 272.7 Da LogP 2.84 TPSA 50.3 ✓ Ro5 ✓ Clean Cc1cccc2c1C(=O)N(C2=O)c3ccnc(c3)Cl
1JY RCSB PDB P0A884 647.6 Da LogP 0.94 TPSA 239.3 2 viol. ✓ Clean C#CCN(c1ccc(cc1)C(=O)NC(CCC(=O)NC(CCC(=O)O)C(=O…
2BR RCSB PDB P0A884 173.0 Da LogP 2.15 TPSA 20.2 ✓ Ro5 ✓ Clean c1ccc(c(c1)O)Br
C2F RCSB PDB P9WFR9 459.5 Da LogP -0.26 TPSA 202.8 1 viol. ✓ Clean C[N@@]1[C@H](CNC2=C1C(=O)NC(=N2)N)CNc3ccc(cc3)C…
CF9 RCSB PDB P0A886 335.3 Da LogP 3.50 TPSA 95.7 ✓ Ro5 ✓ Clean c1cc2c(ccc3c2c(c1)C(=O)O3)OC(=O)c4ccc(cc4)[N+](…
D16 RCSB PDB P0A884 458.5 Da LogP 1.98 TPSA 152.7 ✓ Ro5 ✓ Clean CC1=NC(=O)c2cc(ccc2N1)CN(C)c3ccc(s3)C(=O)N[C@@H…
DDU RCSB PDB P0A884 212.2 Da LogP -0.80 TPSA 84.3 ✓ Ro5 ✓ Clean C[C@@H]1[C@H](C[C@@H](O1)N2C=CC(=O)NC2=O)O
DHF RCSB PDB P0A884 443.4 Da LogP 0.01 TPSA 211.9 1 viol. ✓ Clean c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NCC2=NC3=…
DTT RCSB PDB P0A884 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
DTU RCSB PDB P0A884 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@H]([C@H](CS)O)O)S
DUR RCSB PDB P0A884 228.2 Da LogP -1.82 TPSA 104.6 ✓ Ro5 ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO)O
F89 RCSB PDB P0A884 500.5 Da LogP 3.27 TPSA 152.7 1 viol. ✓ Clean CC1=Nc2ccc3ccc(cc3c2C(=O)N1)CNc4ccc5c(c4)CN(C5=…
FFO RCSB PDB Q834R3 473.4 Da LogP -0.73 TPSA 219.8 1 viol. ✓ Clean c1cc(ccc1C(=O)NC(CCC(=O)O)C(=O)O)NCC2CNC3=C(N2C…
FGT RCSB PDB P07607 318.3 Da LogP 3.56 TPSA 66.8 ✓ Ro5 ✓ Clean c1ccc2c(c1)C(=O)OC2(c3ccc(cc3)O)c4ccc(cc4)O
GA9 RCSB PDB P0A884 560.6 Da LogP 6.89 TPSA 66.8 2 viol. ✓ Clean c1cc2c(ccc3c2c(c1)C(OC3=O)(c4ccc(c(c4)Br)O)c5cc…
LY3 RCSB PDB P0A884 451.4 Da LogP -0.05 TPSA 208.4 1 viol. ✓ Clean c1cc(ccc1CCc2c[nH]c3c2C(=O)NC(=N3)N)C(=O)N[C@@H…
LYA RCSB PDB P9WFR9 427.4 Da LogP 0.67 TPSA 191.3 1 viol. ✓ Clean c1cc(ccc1CCc2c[nH]c3c2C(=O)N=C(N3)N)C(=O)N[C@@H…
LYB RCSB PDB P0A884 814.8 Da LogP -1.28 TPSA 390.5 3 viol. ✓ Clean c1cc(ccc1CCc2c[nH]c3c2C(=O)NC(=N3)N)C(=O)N[C@@H…
LYD RCSB PDB P0A884 397.4 Da LogP 1.46 TPSA 154.0 ✓ Ro5 ✓ Clean CC(C)[C@@H](C(=O)O)NC(=O)c1ccc(cc1)CCc2c[nH]c3c…
MEF RCSB PDB P0A884 457.4 Da LogP -0.52 TPSA 194.0 1 viol. ✓ Clean c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)[N@]2C[C@…
MTX RCSB PDB P0A884 454.4 Da LogP 0.27 TPSA 210.5 ✓ Ro5 ✓ Clean CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)N[C@@…
NDN RCSB PDB P0A884 353.2 Da LogP -1.80 TPSA 194.2 ✓ Ro5 ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)[N+](=O)…
NDU RCSB PDB P0A884 355.2 Da LogP -2.23 TPSA 188.8 ✓ Ro5 ✓ Clean C1[C@@H]([C@H](O[C@H]1N2CC(C(=O)NC2=O)[N+](=O)[…
NOH RCSB PDB P07607 323.2 Da LogP -1.20 TPSA 163.4 ✓ Ro5 ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)NO)COP(=O)(…
PFG RCSB PDB P0A884 864.8 Da LogP -0.76 TPSA 377.9 3 viol. ✓ Clean C#CCN(Cc1ccc2c(c1)C(=O)N=C(N2)N)c3ccc(cc3)C(=O)…
SPM RCSB PDB P9WFR9 202.3 Da LogP -0.36 TPSA 76.1 ✓ Ro5 ✓ Clean C(CCNCCCN)CNCCCN
SS7 RCSB PDB Q834R3 367.4 Da LogP 3.29 TPSA 72.9 ✓ Ro5 ✓ Clean Cc1cc(cc(c1OC[C@H](C)N2C(=O)c3ccccc3C2=O)C)OC(=…
TGQ RCSB PDB P07607 459.5 Da LogP -0.26 TPSA 202.8 1 viol. ✓ Clean CN(C[C@H]1CNC2=C(N1)C(=O)N=C(N2)N)c3ccc(cc3)C(=…
THG RCSB PDB P0A884 445.4 Da LogP -0.28 TPSA 211.6 1 viol. ✓ Clean c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@H]2C…
TMF RCSB PDB P00469 455.4 Da LogP -0.23 TPSA 194.3 ✓ Ro5 ✓ Clean c1cc(ccc1C(=O)N[C@H](CCC(=O)O)C(=O)O)[N@@]2C[C@…
TP2 RCSB PDB P0A884 328.5 Da LogP 1.19 TPSA 66.5 ✓ Ro5 ✓ Clean Cc1ccc(cc1)S(=O)(=O)[N@]2CCC[C@@H]2C(=O)NCCS
TPR RCSB PDB P0A884 269.3 Da LogP 1.23 TPSA 74.7 ✓ Ro5 ✓ Clean Cc1ccc(cc1)S(=O)(=O)[N@]2CCC[C@@H]2C(=O)O
UMC RCSB PDB P0A884 310.2 Da LogP -1.49 TPSA 145.6 ✓ Ro5 ✓ Clean C1CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(…

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Chemistry

ChEMBL CHEMBL349432 ChEMBL CHEMBL320217 ChEMBL CHEMBL102143 ChEMBL CHEMBL61300 ChEMBL CHEMBL30179 ChEMBL CHEMBL299273 ChEMBL CHEMBL1202139 ChEMBL CHEMBL360335 ChEMBL CHEMBL362606 ChEMBL CHEMBL323098 ChEMBL CHEMBL35926 ChEMBL CHEMBL1202137 ChEMBL CHEMBL160498 ChEMBL CHEMBL170933 ChEMBL CHEMBL264807 ChEMBL CHEMBL917 ChEMBL CHEMBL293148 ChEMBL CHEMBL320450 ChEMBL CHEMBL337914 ChEMBL CHEMBL171226 ChEMBL CHEMBL420155 ChEMBL CHEMBL338429 ChEMBL CHEMBL1202138 ChEMBL CHEMBL103105 ChEMBL CHEMBL434602 ChEMBL CHEMBL55437 ChEMBL CHEMBL157459 ChEMBL CHEMBL105346 ChEMBL CHEMBL1202140 ChEMBL CHEMBL157025 ChEMBL CHEMBL436448 ChEMBL CHEMBL355543 ChEMBL CHEMBL37106 ChEMBL CHEMBL58548 ChEMBL CHEMBL126325 ChEMBL CHEMBL126648 ChEMBL CHEMBL439975 ChEMBL CHEMBL425692 ChEMBL CHEMBL341334 ChEMBL CHEMBL127583 ChEMBL CHEMBL60700 ChEMBL CHEMBL126555 ChEMBL CHEMBL3143163 ChEMBL CHEMBL340888 ChEMBL CHEMBL353066 ChEMBL CHEMBL354785 ChEMBL CHEMBL168952 ChEMBL CHEMBL170494 ChEMBL CHEMBL288666 ChEMBL CHEMBL301895 ChEMBL CHEMBL320794 ChEMBL CHEMBL326128 ChEMBL CHEMBL338598 ChEMBL CHEMBL340814 ChEMBL CHEMBL412127 ChEMBL CHEMBL320651 ChEMBL CHEMBL127598 ChEMBL CHEMBL299062 ChEMBL CHEMBL59261 ChEMBL CHEMBL125856 ChEMBL CHEMBL127954 ChEMBL CHEMBL292920 ChEMBL CHEMBL57269 ChEMBL CHEMBL291084 ChEMBL CHEMBL57549 ChEMBL CHEMBL289749 ChEMBL CHEMBL127142 ChEMBL CHEMBL340842 ChEMBL CHEMBL338644 ChEMBL CHEMBL317717 ChEMBL CHEMBL405513 ChEMBL CHEMBL268593 ChEMBL CHEMBL160502 ChEMBL CHEMBL264609 ChEMBL CHEMBL168970 ChEMBL CHEMBL112185 ChEMBL CHEMBL127541 ChEMBL CHEMBL6271 ChEMBL CHEMBL156447 ChEMBL CHEMBL170789 ChEMBL CHEMBL367732 ChEMBL CHEMBL172160 ChEMBL CHEMBL25889 ChEMBL CHEMBL169411 ChEMBL CHEMBL123614 ChEMBL CHEMBL126914 ChEMBL CHEMBL127745 ChEMBL CHEMBL127333 ChEMBL CHEMBL341323 ChEMBL CHEMBL6715 ChEMBL CHEMBL126541 ChEMBL CHEMBL6436 ChEMBL CHEMBL341262 ChEMBL CHEMBL355321 ChEMBL CHEMBL169921 ChEMBL CHEMBL36433 ChEMBL CHEMBL36721 ChEMBL CHEMBL263325 ChEMBL CHEMBL104230 ChEMBL CHEMBL126242