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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

1kmy

2.000 Å

X-ray

2001-12-17

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Biphenyl-2,3-diol 1,2-dioxygenase
ID:BPHC_BURXL
AC:P47228
Organism:Burkholderia xenovorans
Reign:Bacteria
TaxID:266265
EC Number:1.13.11.39


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:18.082
Number of residues:27
Including
Standard Amino Acids: 25
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals: FE2

Cavity properties

LigandabilityVolume (Å3)
0.808398.250

% Hydrophobic% Polar
59.3240.68
According to VolSite

Ligand :
1kmy_1 Structure
HET Code: BPY
Formula: C12H10O2
Molecular weight: 186.207 g/mol
DrugBank ID: DB02923
Buried Surface Area:73.56 %
Polar Surface area: 40.46 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 2
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
22.4927-22.568672.4227


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
CK8CG2VAL- 1484.160Hydrophobic
CK6CD1ILE- 1733.840Hydrophobic
CKACEMET- 1753.80Hydrophobic
DuArDuArHIS- 2413.480Aromatic Face/Face
CK5CBHIS- 2413.930Hydrophobic
OK2OHTYR- 2502.75154.57H-Bond
(Protein Donor)
CK1CBPRO- 2803.930Hydrophobic
OK1FEFE2- 5002.350Metal Acceptor
OK2FEFE2- 5001.980Metal Acceptor