Structure of PDB 1kmy Chain A Binding Site BS02

Receptor Information
>1kmy Chain A (length=288) Species: 266265 (Paraburkholderia xenovorans LB400) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SIRSLGYMGFAVSDVAAWRSFLTQKLGLMEAGTTDNGDLFRIDSRAWRIA
VQQGEVDDLAFAGYEVADAAGLAQMADKLKQAGIAVTTGDASLARRRGVT
GLITFADPFGLPLEIYYGASEVFEKPFLPGAAVSGFLTGEQGLGHFVRCV
PDSDKALAFYTDVLGFQLSDVIDMKMGPDVTVPAYFLHCNERHHTLAIAA
FPLPKRIHHFMLEVASLDDVGFAFDRVDADGLITSTLGRHTNDHMVSFYA
STPSGVEVEYGWSARTVDRSWVVVRHDSPSMWGHKSVR
Ligand information
Ligand IDBPY
InChIInChI=1S/C12H10O2/c13-11-8-4-7-10(12(11)14)9-5-2-1-3-6-9/h1-8,13-14H
InChIKeyYKOQAAJBYBTSBS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Oc1cccc(c2ccccc2)c1O
OpenEye OEToolkits 1.5.0c1ccc(cc1)c2cccc(c2O)O
ACDLabs 10.04Oc2c(c1ccccc1)cccc2O
FormulaC12 H10 O2
NameBIPHENYL-2,3-DIOL
ChEMBL
DrugBankDB02923
ZINCZINC000000901387
PDB chain1kmy Chain A Residue 300 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1kmy Molecular basis for the stabilization and inhibition of 2, 3-dihydroxybiphenyl 1,2-dioxygenase by t-butanol.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		H146 F187 H195 H210 H241 N243 Y250 E260
Binding residue
(residue number reindexed from 1)		H145 F186 H194 H209 H240 N242 Y249 E259
Annotation score5
Binding affinityMOAD: Kd=8uM
PDBbind-CN: -logKd/Ki=5.10,Kd=8uM
Enzymatic activity
Enzyme Commision number 1.13.11.39: biphenyl-2,3-diol 1,2-dioxygenase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005506 iron ion binding
GO:0008198 ferrous iron binding
GO:0018583 biphenyl-2,3-diol 1,2-dioxygenase activity
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
Biological Process
GO:0009056 catabolic process
GO:0042178 xenobiotic catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1kmy, PDBe:1kmy, PDBj:1kmy
PDBsum1kmy
PubMed9857017
UniProtP47228|BPHC_PARXL Biphenyl-2,3-diol 1,2-dioxygenase (Gene Name=bphC)

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