Structure of PDB 2qcm Chain A Binding Site BS01

Receptor Information
>2qcm 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
LGPSICMLKTHVDILNDFTLDVMKELITLAKCHEFLIFENRKFADIGNTV
KKQYEGGIFKIASWADLVNAHVVPGSGVVKGLQEVGLPLHRGCLLIAEMS
STGSLATGDYTRAAVRMAEEHSEFVVGFISGSRVSMKPEFLHLTPGVQLE
AGGDNLGQQYNSPQEVIGKRGSDIIIVGRGIISAADRLEAAEMYRKAAWE
AYLSRLG
Ligand information
Ligand IDJW5
InChIInChI=1S/C10H15N2O10P/c13-2-4-1-6(14)11-10(17)12(4)9-8(16)7(15)5(22-9)3-21-23(18,19)20/h1,5,7-9,13,15-16H,2-3H2,(H,11,14,17)(H2,18,19,20)/t5-,7-,8-,9-/m1/s1
InChIKeyMSQUFEPNTQRBDI-ZOQUXTDFSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1NC(=O)N(C(=C1)CO)C2OC(C(O)C2O)COP(=O)(O)O
OpenEye OEToolkits 1.5.0C1=C(N(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)CO
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)CO
CACTVS 3.341OCC1=CC(=O)NC(=O)N1[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
CACTVS 3.341OCC1=CC(=O)NC(=O)N1[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
FormulaC10 H15 N2 O10 P
Name6-(HYDROXYMETHYL)URIDINE 5'-(DIHYDROGEN PHOSPHATE)
ChEMBL
DrugBank
ZINCZINC000058649740
PDB chain2qcm Chain A 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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PDB2qcm Structures of the human orotidine-5'-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design.
Resolution1.67 Å
Binding residue
(original residue number in PDB)		S257 D259 H283 N312 M371 S372 P417 Q430 Y432 G450 R451
Binding residue
(residue number reindexed from 1)		S35 D37 H61 N90 M149 S150 P195 Q208 Y210 G228 R229
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=3.35,IC50=450uM
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:2qcm, PDBe:2qcm, PDBj:2qcm
PDBsum2qcm
PubMed18184586
UniProtP11172|UMPS_HUMAN Uridine 5'-monophosphate synthase (Gene Name=UMPS)

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