Structure of PDB 2qcd Chain B Binding Site BS02

Receptor Information
>2qcd 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]
AMELSFGARAELPRIHPVASKLLRLMQKKETNLCLSADVSLARELLQLAD
ALGPSICMLKTHVDILNDFTLDVMKELITLAKCHEFLIFEDRKFADIGNT
VKKQYEGGIFKIASWADLVNAHVVPGSGVVKGLQEVGLPLHRGCLLIAEM
SSTGSLATGDYTRAAVRMAEEHSEFVVGFISGSRVSMKPEFLHLTPGVQL
EAGGDNLGQQYNSPQEVIGKRGSDIIIVGRGIISAADRLEAAEMYRKAAW
EAYLSRLG
Ligand information
Ligand IDU5P
InChIInChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyDJJCXFVJDGTHFX-XVFCMESISA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=O)(O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
FormulaC9 H13 N2 O9 P
NameURIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL214393
DrugBankDB03685
ZINCZINC000002123545
PDB chain2qcd Chain B Residue 2 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2qcd Structures of the human orotidine-5'-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design.
Resolution2.03 Å
Binding residue
(original residue number in PDB)		S257 D259 H283 K314 M371 S372 P417 Q430 Y432 G450 R451
Binding residue
(residue number reindexed from 1)		S36 D38 H62 K93 M150 S151 P196 Q209 Y211 G229 R230
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=3.40,IC50=400uM
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:2qcd, PDBe:2qcd, PDBj:2qcd
PDBsum2qcd
PubMed18184586
UniProtP11172|UMPS_HUMAN Uridine 5'-monophosphate synthase (Gene Name=UMPS)

[Back to BioLiP]