Structure of PDB 2zz6 Chain A Binding Site BS01

Receptor Information
>2zz6 Chain A (length=215) Species: 145262 (Methanothermobacter thermautotrophicus) [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 ID6AZ
InChIInChI=1S/C9H12N5O9P/c10-13-12-4-1-5(15)11-9(18)14(4)8-7(17)6(16)3(23-8)2-22-24(19,20)21/h1,3,6-8,16-17H,2H2,(H,11,15,18)(H2,19,20,21)/t3-,6-,7-,8-/m1/s1
InChIKeyGBBWDDPNGBRVEX-YXZULKJRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=C(N(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)N=[N+]=[N-]
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C(=O)NC(=O)C=C2N=[N+]=[N-]
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C(=O)NC(=O)C=C2N=[N+]=[N-]
ACDLabs 10.04[N-]=[N+]=N\C=1N(C(=O)NC(=O)C=1)C2OC(C(O)C2O)COP(=O)(O)O
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)N=[N+]=[N-]
FormulaC9 H12 N5 O9 P
Name6-azidouridine 5'-(dihydrogen phosphate);
6-AZIDO-UMP
ChEMBLCHEMBL463623
DrugBank
ZINCZINC000014975887
PDB chain2zz6 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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PDB2zz6 Structural characterization of the molecular events during a slow substrate-product transition in orotidine 5'-monophosphate decarboxylase
Resolution1.66 Å
Binding residue
(original residue number in PDB)		D20 K72 M126 S127 P180 Q185 G202 R203
Binding residue
(residue number reindexed from 1)		D10 K62 M116 S117 P170 Q175 G192 R193
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=6.72,Ki=0.19uM
BindingDB: Ki=190nM
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:2zz6, PDBe:2zz6, PDBj:2zz6
PDBsum2zz6
PubMed19236876
UniProtO26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

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