Structure of PDB 3n3y Chain A Binding Site BS04

Receptor Information
>3n3y Chain A (length=209) Species: 102617 (Helicobacter pylori SS1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FMEVICKHYTPLDIASQAIRTCWQSFEYSDDGGCKDKELIHRVGNIFRHS
STLEHLYYNFEIKGLSRGALQELSRHRIASLSVKSSRYTLRELKEVESFL
PLNETNLERAREFLVFVDNEKVNAMSVLALENLRVLLSEHNIKNDLAKYA
MPESYKTHLAYSINARSLQNLLTLRSSNKALKEMQDLAKALFDALPGEHQ
YLFEDCLKH
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 B Residue 304 [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)		E71 R74 R174
Binding residue
(residue number reindexed from 1)		E72 R75 R175
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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