Structure of PDB 3g1v Chain A Binding Site BS01

Receptor Information
>3g1v Chain A (length=213) Species: 187420 (Methanothermobacter thermautotrophicus str. Delta H) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFR
KRFGCRIIAGFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACL
NVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTR
PERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADN
PAAAAAGIIESIK
Ligand information
Ligand ID5FU
InChIInChI=1S/C9H12FN2O9P/c10-3-1-12(9(16)11-7(3)15)8-6(14)5(13)4(21-8)2-20-22(17,18)19/h1,4-6,8,13-14H,2H2,(H,11,15,16)(H2,17,18,19)/t4-,5-,6-,8-/m1/s1
InChIKeyRNBMPPYRHNWTMA-UAKXSSHOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=C(C(=O)NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)F
OpenEye OEToolkits 1.5.0C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)F
ACDLabs 10.04FC=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2O)COP(=O)(O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=C(F)C(=O)NC2=O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(F)C(=O)NC2=O
FormulaC9 H12 F N2 O9 P
Name5-FLUORO-URIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL474163
DrugBank
ZINC
PDB chain3g1v Chain A Residue 501 [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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PDB3g1v Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.
Resolution1.3 Å
Binding residue
(original residue number in PDB)		D20 K42 L123 M126 S127 P180 Q185 G202 R203
Binding residue
(residue number reindexed from 1)		D10 K32 L113 M116 S117 P170 Q175 G192 R193
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=3.19,Ki=645uM
BindingDB: Ki=645000nM
Enzymatic activity
Catalytic site (original residue number in PDB) K42 G70 K72 D75
Catalytic site (residue number reindexed from 1) K32 G60 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

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3g1v, PDBe:3g1v, PDBj:3g1v
PDBsum3g1v
PubMed19435314
UniProtO26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

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