Structure of PDB 4o8r Chain A Binding Site BS02

Receptor Information
>4o8r Chain A (length=220) Species: 145262 (Methanothermobacter thermautotrophicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RVDVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMD
IIAEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGAD
SVRACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNY
VGPSTRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRS
IYLADNPAAAAAGIIESIKD
Ligand information
Ligand IDH2U
InChIInChI=1S/C9H15N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h4,6-8,13-14H,1-3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyNBWDKGJHOHJBRJ-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
OpenEye OEToolkits 1.5.0C1CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](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)N2CCC(=O)NC2=O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2CCC(=O)NC2=O
ACDLabs 10.04O=C1N(CCC(=O)N1)C2OC(C(O)C2O)COP(=O)(O)O
FormulaC9 H15 N2 O9 P
Name5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
ChEMBL
DrugBank
ZINC
PDB chain4o8r Chain B Residue 301 [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]
PDB4o8r Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 5,6-dihydrouridine 5'-monophosphate
Resolution2.293 Å
Binding residue
(original residue number in PDB)		D75 I76 T79
Binding residue
(residue number reindexed from 1)		D71 I72 T75
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) K42 D70 K72 D75
Catalytic site (residue number reindexed from 1) K38 D66 K68 D71
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:4o8r, PDBe:4o8r, PDBj:4o8r
PDBsum4o8r
PubMed
UniProtO26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

[Back to BioLiP]