Structure of PDB 3ex2 Chain A Binding Site BS02

Receptor Information
>3ex2 Chain A (length=257) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MELSFGARAELPRIHPVASKLLRLMQKKETNLCLSADVSLARELLQLADA
LGPSICMLKTHVDILNDFTLDVMKELITLAKCHEFLIFEDRKFADIGNTV
KKQYEGGIFKIASWADLVNAHVVPGSGVVKGLQEVGLPLHRGCLLIAEMS
STGSLATGDYTRAAVRMAEEHSEFVVGFISGSRVSMKPEFLHLTPGVQLE
AGGDNLGQQYNSPQEVIGKRGSDIIIVGRGIISAADRLEAAEMYRKAAWE
AYLSRLG
Ligand information
Ligand ID6CN
InChIInChI=1S/C10H12N3O9P/c11-2-4-1-6(14)12-10(17)13(4)9-8(16)7(15)5(22-9)3-21-23(18,19)20/h1,5,7-9,15-16H,3H2,(H,12,14,17)(H2,18,19,20)/t5-,7-,8-,9-/m1/s1
InChIKeyGCVKNFUDFHDSJQ-ZOQUXTDFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=C(N(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)C#N
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C(=O)NC(=O)C=C2C#N
ACDLabs 10.04N#CC=1N(C(=O)NC(=O)C=1)C2OC(C(O)C2O)COP(=O)(O)O
OpenEye OEToolkits 1.5.0C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)C#N
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C(=O)NC(=O)C=C2C#N
FormulaC10 H12 N3 O9 P
Name6-cyanouridine 5'-phosphate
ChEMBLCHEMBL512577
DrugBank
ZINC
PDB chain3ex2 Chain B Residue 481 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3ex2 Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase
Resolution1.55 Å
Binding residue
(original residue number in PDB)		D317 I318 T321
Binding residue
(residue number reindexed from 1)		D95 I96 T99
Annotation score2
Binding affinityMOAD: ic50~200uM
PDBbind-CN: -logKd/Ki=3.70,IC50=200uM
Enzymatic activity
Enzyme Commision number 2.4.2.10: orotate phosphoribosyltransferase.
4.1.1.23: orotidine-5'-phosphate decarboxylase.
Gene Ontology
Molecular Function
GO:0004590 orotidine-5'-phosphate decarboxylase activity
Biological Process
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
GO:0044205 'de novo' UMP biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3ex2, PDBe:3ex2, PDBj:3ex2
PDBsum3ex2
PubMed19472232
UniProtP11172|UMPS_HUMAN Uridine 5'-monophosphate synthase (Gene Name=UMPS)

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