Structure of PDB 2cze Chain A Binding Site BS01

Receptor Information
>2cze Chain A (length=208) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIVLALDVYEGERAIKIAKSVKDYISMIKVNWPLILGSGVDIIRRLKEET
GVEIIADLKLADIPNTNRLIARKVFGAGADYVIVHTFVGRDSVMAVKELG
EIIMVVEMSHPGALEFINPLTDRFIEVANEIEPFGVIAPGTRPERIGYIR
DRLKEGIKILAPGIGAQGGKAKDAVKAGADYIIVGRAIYNAPNPREAAKA
IYDEIRGV
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 chain2cze Chain A Residue 401 [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]
PDB2cze Crystal structure of orotidine 5'-phosphate decarboxylase from Pyrococcus horikoshii OT3 complexed with UMP
Resolution1.85 Å
Binding residue
(original residue number in PDB)		D7 K29 N31 D57 K59 M108 S109 P162 Q167 G185 R186
Binding residue
(residue number reindexed from 1)		D7 K29 N31 D57 K59 M108 S109 P162 Q167 G185 R186
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K29 D57 K59 D62
Catalytic site (residue number reindexed from 1) K29 D57 K59 D62
Enzyme Commision number 4.1.1.23: orotidine-5'-phosphate decarboxylase.
Gene Ontology
Molecular Function
GO:0004590 orotidine-5'-phosphate decarboxylase activity
GO:0016831 carboxy-lyase activity
Biological Process
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
GO:0006221 pyrimidine nucleotide biosynthetic process
GO:0044205 'de novo' UMP biosynthetic process
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2cze, PDBe:2cze, PDBj:2cze
PDBsum2cze
PubMed
UniProtO58462|PYRF_PYRHO Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

[Back to BioLiP]