Structure of PDB 3ex2 Chain B Binding Site BS02

Receptor Information
>3ex2 Chain B (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)		S257 D259 K281 H283 D312 K314 M371 S372 P417 Q430 Y432 G450 R451
Binding residue
(residue number reindexed from 1)		S35 D37 K59 H61 D90 K92 M149 S150 P195 Q208 Y210 G228 R229
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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