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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:

4wbo

2.810 Å

X-ray

2014-09-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Rhodopsin kinase
ID:RK_BOVIN
AC:P28327
Organism:Bos taurus
Reign:Eukaryota
TaxID:9913
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
D100 %


Ligand binding site composition:

B-Factor:87.708
Number of residues:30
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.931884.250

% Hydrophobic% Polar
40.8459.16
According to VolSite

Ligand :
4wbo_4 Structure
HET Code: ANW
Formula: C16H13N2O4
Molecular weight: 297.285 g/mol
DrugBank ID: DB01025
Buried Surface Area:52.03 %
Polar Surface area: 105.34 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 1
Rings: 3
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
-16.5671-62.0317-7.54177


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
CAECBLEU- 1934.490Hydrophobic
CAGCBLEU- 1933.980Hydrophobic
CAHCD1LEU- 1934.060Hydrophobic
CAJCD1LEU- 1933.80Hydrophobic
CAKCD2LEU- 1933.60Hydrophobic
NABOTHR- 2652.88161.3H-Bond
(Ligand Donor)
CAJCG1ILE- 2664.410Hydrophobic
OASNMET- 2673.32155.17H-Bond
(Protein Donor)
CANCD1LEU- 3213.490Hydrophobic
CAECBALA- 4783.30Hydrophobic
OAUOHOH- 7052.98179.96H-Bond
(Protein Donor)