Structure of PDB 3n3y Chain C Binding Site BS02

Receptor Information
>3n3y Chain C (length=208) Species: 102617 (Helicobacter pylori SS1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FMEVICKHYTPLDIASQAIRTCWQSFEYSDGGCKDKELIHRVGNIFRHSS
TLEHLYYNFEIKGLSRGALQELSRHRIASLSVKSSRYTLRELKEVESFLP
LNETNLERAREFLVFVDNEKVNAMSVLALENLRVLLSEHNIKNDLAKYAM
PESYKTHLAYSINARSLQNLLTLRSSNKALKEMQDLAKALFDALPGEHQY
LFEDCLKH
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 chain3n3y Chain C Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3n3y Structure, Enzymatic Characterization and Inhibitor Discovery of Thymidylate Synthase X (ThyX) from Helicobacter pylori Strain SS1
Resolution2.307 Å
Binding residue
(original residue number in PDB)		R66 V82 S84 S85 R86
Binding residue
(residue number reindexed from 1)		R66 V82 S84 S85 R86
Annotation score3
Enzymatic activity
Enzyme Commision number 2.1.1.148: thymidylate synthase (FAD).
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004799 thymidylate synthase activity
GO:0008168 methyltransferase activity
GO:0050660 flavin adenine dinucleotide binding
GO:0050797 thymidylate synthase (FAD) activity
GO:0070402 NADPH binding
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:3n3y, PDBe:3n3y, PDBj:3n3y
PDBsum3n3y
PubMed
UniProtQ5UVJ4

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