Structure of PDB 4a7x Chain E Binding Site BS01

Receptor Information
>4a7x Chain E (length=227) Species: 85962 (Helicobacter pylori 26695) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NKRVLVKFSGEALAGDNQFGIDIHVLDHIAKEIKSLVENDIEVGIVIGGG
NIIRGVSAAQGGIIRRTSGDYMGMLATVINAVAMQEALEHIGLDTRVQSA
IEIKEICESYIYRKAIRHLEKGRVVIFGAGTGNPFFTTDTAATLRAIEIG
SDLIIKATKVDGIYDKDKKLDTLSYNDALIGDIEVMDDTAISLAKDNKLP
IVVCNMFKKGNLLQVIKHQQGVFSMVK
Ligand information
Ligand IDUDP
InChIInChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyXCCTYIAWTASOJW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.370O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
FormulaC9 H14 N2 O12 P2
NameURIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL130266
DrugBankDB03435
ZINCZINC000004490939
PDB chain4a7x Chain E Residue 1241 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4a7x Structures of Helicobacter Pylori Uridylate Kinase: Insight Into Release of the Product Udp
Resolution2.49 Å
Binding residue
(original residue number in PDB)		E17 G54 G55 G56 G61 D76 G79 M80 T83 G136 T137 N139 F142 T144
Binding residue
(residue number reindexed from 1)		E11 G48 G49 G50 G55 D70 G73 M74 T77 G130 T131 N133 F136 T138
Annotation score3
Enzymatic activity
Enzyme Commision number 2.7.4.22: UMP kinase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0009041 UMP/dUMP kinase activity
GO:0016301 kinase activity
GO:0033862 UMP kinase activity
Biological Process
GO:0006221 pyrimidine nucleotide biosynthetic process
GO:0006225 UDP biosynthetic process
GO:0016310 phosphorylation
GO:0044210 'de novo' CTP biosynthetic process
GO:0046940 nucleoside monophosphate phosphorylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4a7x, PDBe:4a7x, PDBj:4a7x
PDBsum4a7x
PubMed22751662
UniProtP56106|PYRH_HELPY Uridylate kinase (Gene Name=pyrH)

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