Structure of PDB 3g1f Chain D Binding Site BS02

Receptor Information
>3g1f Chain D (length=215) 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
KRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACL
NVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTR
PERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADN
PAAAAAGIIESIKDL
Ligand information
Ligand ID2OM
InChIInChI=1S/C10H15N2O11P/c13-5-1-3(9(16)17)12(10(18)11-5)8-7(15)6(14)4(23-8)2-22-24(19,20)21/h3-4,6-8,14-15H,1-2H2,(H,16,17)(H,11,13,18)(H2,19,20,21)/t3-,4-,6-,7-,8-/m1/s1
InChIKeyZVESSEXVBFSYOC-NFTAXOAUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1C(N(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)C(=O)O
OpenEye OEToolkits 1.5.0C1[C@@H](N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)C(=O)O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2[C@H](CC(=O)NC2=O)C(O)=O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2[CH](CC(=O)NC2=O)C(O)=O
ACDLabs 10.04O=C(O)C1N(C(=O)NC(=O)C1)C2OC(C(O)C2O)COP(=O)(O)O
FormulaC10 H15 N2 O11 P
Name5,6-dihydroorotidine 5'-monophosphate
ChEMBL
DrugBank
ZINCZINC000058633028
PDB chain3g1f Chain D Residue 229 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3g1f Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		D20 K42 D70 K72 M126 S127 P180 Q185 G202 R203
Binding residue
(residue number reindexed from 1)		D10 K32 D60 K62 M116 S117 P170 Q175 G192 R193
Annotation score2
Binding affinityMOAD: Ki=100uM
Enzymatic activity
Catalytic site (original residue number in PDB) K42 D70 K72 D75
Catalytic site (residue number reindexed from 1) K32 D60 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:3g1f, PDBe:3g1f, PDBj:3g1f
PDBsum3g1f
PubMed19435314
UniProtO26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

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