Structure of PDB 5noo Chain B Binding Site BS01

Receptor Information
>5noo Chain B (length=287) Species: 6239 (Caenorhabditis elegans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QVHLNQDEYKYLKQVEQILREGTRRDDRTGTGTISIFGMQSKYCLRNGTI
PLLTTKRVYWKGVLEELLWFISGSTDGKLLMEKNVKIWEKNGDRAFLDNL
GFTSREEGDLGPVYGFQWRHFGAKYVDCHTDYSGQGVDQLAEVIRQIKEQ
PDSRRIIMSAWNPSDLGQMVLPPCHTMCQFYVDNGELSCQLYQRSGDMGL
GVPFNLASYGLLTHMIAKVCGLKPGTLVHTLGDAHVYSNHVDALKIQLDR
EPYAFPKIRFTRDVASIDDFTSDMIALDDYKCHPKIP
Ligand information
Ligand IDUMP
InChIInChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKeyJSRLJPSBLDHEIO-SHYZEUOFSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
CACTVS 3.370O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
CACTVS 3.370O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
FormulaC9 H13 N2 O8 P
Name2'-DEOXYURIDINE 5'-MONOPHOSPHATE;
DUMP
ChEMBLCHEMBL211312
DrugBankDB03800
ZINCZINC000004228260
PDB chain5noo Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5noo Crystal structures of nematode (parasitic T. spiralis and free living C. elegans), compared to mammalian, thymidylate synthases (TS). Molecular docking and molecular dynamics simulations in search for nematode-specific inhibitors of TS.
Resolution2.9 Å
Binding residue
(original residue number in PDB)
R177 R178
Binding residue
(residue number reindexed from 1)
R154 R155
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) E89 W111 Y137 C197 R217 D220
Catalytic site (residue number reindexed from 1) E66 W88 Y114 C174 R194 D197
Enzyme Commision number 2.1.1.45: thymidylate synthase.
Gene Ontology
Molecular Function
GO:0004799 thymidylate synthase activity
GO:0008168 methyltransferase activity
GO:0016741 transferase activity, transferring one-carbon groups
Biological Process
GO:0006231 dTMP biosynthetic process
GO:0006235 dTTP biosynthetic process
GO:0009165 nucleotide biosynthetic process
GO:0032259 methylation

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:5noo, PDBe:5noo, PDBj:5noo
PDBsum5noo
PubMed28826032
UniProtQ9Y052

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