Structure of PDB 1km2 Chain A Binding Site BS01

Receptor Information
>1km2 Chain A (length=211) Species: 145262 (Methanothermobacter thermautotrophicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFRK
RFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACLN
VAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTRP
ERLSRLREIIGQDSFLISPGVGAAGGDPGETLRFADAIIVGRSIYLADNP
AAAAAGIIESI
Ligand information
Ligand IDUP6
InChIInChI=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
InChIKeyLRVZOSYMNMNQFR-SHUUEZRQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=NN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2N=CC(=O)NC2=O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2N=CC(=O)NC2=O
OpenEye OEToolkits 1.5.0C1=NN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
ACDLabs 10.04O=C1N(N=CC(=O)N1)C2OC(C(O)C2O)COP(=O)(O)O
FormulaC8 H12 N3 O9 P
Name6-AZA URIDINE 5'-MONOPHOSPHATE;
6-AZA-UMP
ChEMBLCHEMBL463480
DrugBankDB03718
ZINCZINC000012503861
PDB chain1km2 Chain A Residue 2001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1km2 Mapping the active site-ligand interactions of orotidine 5'-monophosphate decarboxylase by crystallography.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		D20 K42 K72 M126 S127 P180 G202 R203
Binding residue
(residue number reindexed from 1)		D9 K31 K61 M115 S116 P169 G191 R192
Annotation score2
Binding affinityBindingDB: Ki=12400nM
Enzymatic activity
Catalytic site (original residue number in PDB) K42 D70 K72 D75
Catalytic site (residue number reindexed from 1) K31 D59 K61 D64
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
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Biological Process
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Cellular Component
External links
PDB RCSB:1km2, PDBe:1km2, PDBj:1km2
PDBsum1km2
PubMed11900543
UniProtO26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

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