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Structure of PDB 3ewz Chain B Binding Site BS02

Receptor Information
>3ewz Chain B (length=258) 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
AYLSRLGV
Ligand information
Ligand IDCNU
InChIInChI=1S/C10H12N3O9P/c11-1-4-2-13(10(17)12-8(4)16)9-7(15)6(14)5(22-9)3-21-23(18,19)20/h2,5-7,9,14-15H,3H2,(H,12,16,17)(H2,18,19,20)/t5-,6-,7-,9-/m1/s1
InChIKeyBUHKUGLYORHFNN-JXOAFFINSA-N
SMILES
SoftwareSMILES
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C#N)C(=O)NC2=O
OpenEye OEToolkits 1.5.0C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)C#N
ACDLabs 10.04N#CC=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2O)COP(=O)(O)O
OpenEye OEToolkits 1.5.0C1=C(C(=O)NC(=O)N1C2C(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=C(C#N)C(=O)NC2=O
FormulaC10 H12 N3 O9 P
Name5-CYANO-URIDINE-5'-MONOPHOSPHATE;
5-cyano-UMP;
5-cyanouridine 5'-(dihydrogen phosphate)
ChEMBLCHEMBL1164065
DrugBank
ZINCZINC000049802347
PDB chain3ewz Chain B Residue 482 [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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PDB3ewz Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase
Resolution1.4 Å
Binding residue
(original residue number in PDB)		S257 D259 K281 H283 D312 I368 M371 S372 I401 P417 Q430 Y432 G450 R451
Binding residue
(residue number reindexed from 1)		S35 D37 K59 H61 D90 I146 M149 S150 I179 P195 Q208 Y210 G228 R229
Annotation score3
Binding affinityMOAD: ic50=79uM
PDBbind-CN: -logKd/Ki=4.10,IC50=79uM
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:3ewz, PDBe:3ewz, PDBj:3ewz
PDBsum3ewz
PubMed19472232
UniProtP11172|UMPS_HUMAN Uridine 5'-monophosphate synthase (Gene Name=UMPS)

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