Structure of PDB 3qez Chain B Binding Site BS02

Receptor Information
>3qez Chain B (length=218) Species: 187420 (Methanothermobacter thermautotrophicus str. Delta H) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAE
FRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRA
CLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPS
VRPERLSRLREIIGQDSFLISPGAGAQGGDPGETLRFADAIIVGRSIYLA
DNPAAAAAGIIESIKDLL
Ligand information
Ligand IDBMP
InChIInChI=1S/C9H13N2O10P/c12-4-1-5(13)11(9(16)10-4)8-7(15)6(14)3(21-8)2-20-22(17,18)19/h1,3,6-8,13-15H,2H2,(H,10,12,16)(H2,17,18,19)/t3-,6-,7-,8-/m1/s1
InChIKeyUDOBICLZEKUKCV-YXZULKJRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)O
OpenEye OEToolkits 1.5.0C1=C(N(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C(=O)NC(=O)C=C2O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C(=O)NC(=O)C=C2O
ACDLabs 10.04O=C1NC(=O)N(C(O)=C1)C2OC(C(O)C2O)COP(=O)(O)O
FormulaC9 H13 N2 O10 P
Name6-HYDROXYURIDINE-5'-PHOSPHATE
ChEMBLCHEMBL383923
DrugBankDB02890
ZINCZINC000024479522
PDB chain3qez Chain B Residue 229 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3qez Conformational changes in orotidine 5'-monophosphate decarboxylase: a structure-based explanation for how the 5'-phosphate group activates the enzyme.
Resolution1.5431 Å
Binding residue
(original residue number in PDB)		D20 K42 K72 M126 S127 P180 Q185 G202 R203
Binding residue
(residue number reindexed from 1)		D12 K34 K64 M118 S119 P172 Q177 G194 R195
Annotation score3
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:3qez, PDBe:3qez, PDBj:3qez
PDBsum3qez
PubMed23030629
UniProtO26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

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