Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

4kb8

1.950 Å

X-ray

2013-04-23

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Casein kinase I isoform delta
ID:KC1D_HUMAN
AC:P48730
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.11.1


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:40.881
Number of residues:28
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.160452.250

% Hydrophobic% Polar
51.4948.51
According to VolSite

Ligand :
4kb8_2 Structure
HET Code: 1QO
Formula: C16H14N4
Molecular weight: 262.309 g/mol
DrugBank ID: -
Buried Surface Area:67.16 %
Polar Surface area: 50.7 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 1
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
22.257923.8921-47.9372


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
C4CD1ILE- 1540Hydrophobic
C4CG2ILE- 234.150Hydrophobic
C8CD1ILE- 234.30Hydrophobic
C6CG2ILE- 234.060Hydrophobic
C14CG1ILE- 234.250Hydrophobic
C16CBALA- 363.730Hydrophobic
C13CDLYS- 384.340Hydrophobic
C14CBLYS- 383.670Hydrophobic
C1CBPRO- 663.890Hydrophobic
C14CEMET- 803.960Hydrophobic
C16CBMET- 823.320Hydrophobic
C15CGMET- 823.470Hydrophobic
N1OGLU- 833.14163.39H-Bond
(Ligand Donor)
C1CD1LEU- 853.940Hydrophobic
N2NLEU- 853.16153.44H-Bond
(Protein Donor)
C4CD2LEU- 1353.80Hydrophobic
C6CD2LEU- 1353.980Hydrophobic
C6CD1ILE- 1484.30Hydrophobic
C1CG2ILE- 1484.340Hydrophobic
C8CD1ILE- 1484.430Hydrophobic
N4OHOH- 5252.91158.67H-Bond
(Ligand Donor)