Structure of PDB 1km0 Chain B Binding Site BS01
Receptor Information
>1km0 Chain B (length=212) Species:
145262
(Methanothermobacter thermautotrophicus) [
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VMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFR
KRFGCRIIANFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACL
NVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTR
PERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADN
PAAAAAGIIESI
Ligand information
Ligand ID
UP6
InChI
InChI=1S/C8H12N3O9P/c12-4-1-9-11(8(15)10-4)7-6(14)5(13)3(20-7)2-19-21(16,17)18/h1,3,5-7,13-14H,2H2,(H,10,12,15)(H2,16,17,18)/t3-,5-,6-,7-/m1/s1
InChIKey
LRVZOSYMNMNQFR-SHUUEZRQSA-N
SMILES
Software
SMILES
OpenEye OEToolkits 1.5.0
C1=NN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341
O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2N=CC(=O)NC2=O
CACTVS 3.341
O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2N=CC(=O)NC2=O
OpenEye OEToolkits 1.5.0
C1=NN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
ACDLabs 10.04
O=C1N(N=CC(=O)N1)C2OC(C(O)C2O)COP(=O)(O)O
Formula
C8 H12 N3 O9 P
Name
6-AZA URIDINE 5'-MONOPHOSPHATE;
6-AZA-UMP
ChEMBL
CHEMBL463480
DrugBank
DB03718
ZINC
ZINC000012503861
PDB chain
1km0 Chain A Residue 5001 [
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Receptor-Ligand Complex Structure
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PDB
1km0
Mapping the active site-ligand interactions of orotidine 5'-monophosphate decarboxylase by crystallography.
Resolution
1.7 Å
Binding residue
(original residue number in PDB)
D75 I76 T79
Binding residue
(residue number reindexed from 1)
D65 I66 T69
Annotation score
2
Binding affinity
BindingDB: Ki=12400nM
Enzymatic activity
Catalytic site (original residue number in PDB)
K42 N70 K72 D75
Catalytic site (residue number reindexed from 1)
K32 N60 K62 D65
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
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Molecular Function
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Biological Process
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Cellular Component
External links
PDB
RCSB:1km0
,
PDBe:1km0
,
PDBj:1km0
PDBsum
1km0
PubMed
11900543
UniProt
O26232
|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)
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