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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:

1kw9

1.950 Å

X-ray

2002-01-29

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Biphenyl-2,3-diol 1,2-dioxygenase
ID:BPHC_PSES1
AC:P17297
Organism:Pseudomonas sp.
Reign:Bacteria
TaxID:307
EC Number:1.13.11.39


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:15.732
Number of residues:28
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: FE2

Cavity properties

LigandabilityVolume (Å3)
0.796384.750

% Hydrophobic% Polar
45.6154.39
According to VolSite

Ligand :
1kw9_1 Structure
HET Code: BPY
Formula: C12H10O2
Molecular weight: 186.207 g/mol
DrugBank ID: DB02923
Buried Surface Area:72.79 %
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
83.339338.469616.4549


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- 1474.060Hydrophobic
CK6CD1ILE- 1723.810Hydrophobic
CK9CD1ILE- 1744.060Hydrophobic
DuArDuArHIS- 2403.410Aromatic Face/Face
CK5CBHIS- 2404.060Hydrophobic
OK2OHTYR- 2492.6163.4H-Bond
(Protein Donor)
CK1CBTHR- 2803.850Hydrophobic
CKCCG2THR- 2803.730Hydrophobic
OK1FEFE2- 3012.170Metal Acceptor
OK2FEFE2- 3012.020Metal Acceptor