Structure of PDB 3wjw Chain A Binding Site BS01

Receptor Information
>3wjw Chain A (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 IDU6M
InChIInChI=1S/C10H15N2O9P/c1-4-2-6(13)11-10(16)12(4)9-8(15)7(14)5(21-9)3-20-22(17,18)19/h2,5,7-9,14-15H,3H2,1H3,(H,11,13,16)(H2,17,18,19)/t5-,7-,8-,9-/m1/s1
InChIKeyCHBBJHPQYVYKFI-ZOQUXTDFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC1=CC(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1C)C(O)C2O
OpenEye OEToolkits 1.7.6CC1=CC(=O)NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.385CC1=CC(=O)NC(=O)N1[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
CACTVS 3.385CC1=CC(=O)NC(=O)N1[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
FormulaC10 H15 N2 O9 P
Name6-methyluridine 5'-(dihydrogen phosphate)
ChEMBLCHEMBL472783
DrugBank
ZINCZINC000014975893
PDB chain3wjw Chain A Residue 301 [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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PDB3wjw Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase.
Resolution1.59 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=134uM
PDBbind-CN: -logKd/Ki=3.87,Ki=134uM
BindingDB: Ki=134000nM
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:3wjw, PDBe:3wjw, PDBj:3wjw
PDBsum3wjw
PubMed24151964
UniProtO26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

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