Structure of PDB 1km0 Chain B Binding Site BS02
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 B Residue 5002 [
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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)
D20 K42 N70 K72 M126 S127 P180 Q185 G202 R203
Binding residue
(residue number reindexed from 1)
D10 K32 N60 K62 M116 S117 P170 Q175 G192 R193
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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