Structure of PDB 4dq1 Chain B Binding Site BS02

Receptor Information
>4dq1 Chain B (length=300) Species: 158878 (Staphylococcus aureus subsp. aureus Mu50) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NSFDAAYHSLCEEVLEIGNTRNDRTNTGTISKFGHQLRFDLSKGFPLLTT
KKVSFKLVATELLWFIKGDTNIQYLLKYNNNIWNEWAFENYIKSDEYNGP
DMFNEQYKEQMKQFKQRILEDDTFAKQFGDLGNVYGKQWRDWVDKDGNHF
DQLKTVIEQIKHNPDSRRHIVSAWNPTEIDTMALPPCHTMFQFYVQDGKL
SCQLYQRSADIFLGVPFNIASYALLTHLIAKECGLEVGEFVHTFGDAHIY
SNHIDAIQTQLARESFNPPTLKINSDKSIFDINYEDLEIVDYESHPAIKA
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 chain4dq1 Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4dq1 Thymidylate synthase from Staphylococcus aureus.
Resolution2.71 Å
Binding residue
(original residue number in PDB)		R26 C201 Q220 R221 S222 A223 D224 N232 H262 Y264
Binding residue
(residue number reindexed from 1)		R24 C187 Q206 R207 S208 A209 D210 N218 H248 Y250
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) E63 W85 Y149 C201 R221 D224
Catalytic site (residue number reindexed from 1) E61 W83 Y135 C187 R207 D210
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
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4dq1, PDBe:4dq1, PDBj:4dq1
PDBsum4dq1
PubMed
UniProtP67046|TYSY_STAAM Thymidylate synthase (Gene Name=thyA)

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