Structure of PDB 3nqf Chain A Binding Site BS02

Receptor Information
>3nqf Chain A (length=219) Species: 145262 (Methanothermobacter thermautotrophicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIA
EFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVR
ACLNVAEEMGREVFLSTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGP
STRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYL
ADNPAAAAAGIIESIKDLL
Ligand information
Ligand IDBMP
InChIInChI=1S/C9H13N2O10P/c12-4-1-5(13)11(9(16)10-4)8-7(15)6(14)3(21-8)2-20-22(17,18)19/h1,3,6-8,13-15H,2H2,(H,10,12,16)(H2,17,18,19)/t3-,6-,7-,8-/m1/s1
InChIKeyUDOBICLZEKUKCV-YXZULKJRSA-N
SMILES
SoftwareSMILES
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)O
OpenEye OEToolkits 1.5.0C1=C(N(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C(=O)NC(=O)C=C2O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C(=O)NC(=O)C=C2O
ACDLabs 10.04O=C1NC(=O)N(C(O)=C1)C2OC(C(O)C2O)COP(=O)(O)O
FormulaC9 H13 N2 O10 P
Name6-HYDROXYURIDINE-5'-PHOSPHATE
ChEMBLCHEMBL383923
DrugBankDB02890
ZINCZINC000024479522
PDB chain3nqf Chain B Residue 229 [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]
PDB3nqf Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: importance of residues in the orotate binding site.
Resolution1.312 Å
Binding residue
(original residue number in PDB)		D75 I76 T79
Binding residue
(residue number reindexed from 1)		D68 I69 T72
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K42 D70 K72 D75
Catalytic site (residue number reindexed from 1) K35 D63 K65 D68
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:3nqf, PDBe:3nqf, PDBj:3nqf
PDBsum3nqf
PubMed21870810
UniProtO26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

[Back to BioLiP]