Structure of PDB 1dvj Chain A Binding Site BS01

Receptor Information
>1dvj Chain A (length=239) Species: 145262 (Methanothermobacter thermautotrophicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAE
FRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRA
CLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPS
TRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLA
DNPAAAAAGIIESIKDLLIPEDPAANKARKEAELAAATA
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 chain1dvj Chain A Residue 5001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1dvj Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase.
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)		D12 K34 K64 M118 S119 P172 G194 R195
Annotation score2
Binding affinityMOAD: Ki=0.51mM
BindingDB: Ki=12400nM
Enzymatic activity
Catalytic site (original residue number in PDB) K42 D70 K72 D75
Catalytic site (residue number reindexed from 1) K34 D62 K64 D67
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:1dvj, PDBe:1dvj, PDBj:1dvj
PDBsum1dvj
PubMed10681441
UniProtO26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

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