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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:

4kio

2.180 Å

X-ray

2013-05-02

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Tyrosine-protein kinase ITK/TSK
ID:ITK_HUMAN
AC:Q08881
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.10.2


Chains:

Chain Name:Percentage of Residues
within binding site
B83 %
D17 %


Ligand binding site composition:

B-Factor:37.775
Number of residues:35
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.5172041.875

% Hydrophobic% Polar
36.2063.80
According to VolSite

Ligand :
4kio_2 Structure
HET Code: G5K
Formula: C22H27N8O2S
Molecular weight: 467.567 g/mol
DrugBank ID: -
Buried Surface Area:58.39 %
Polar Surface area: 137.84 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 3
Rings: 5
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 7

Mass center Coordinates

XYZ
12.667313.516669.0515


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
C17CGGLN- 3673.80Hydrophobic
C19CGGLN- 3673.850Hydrophobic
C17CG2ILE- 3694.340Hydrophobic
C19CG2ILE- 3694.180Hydrophobic
C21CD1ILE- 3694.340Hydrophobic
C7CG2VAL- 3774.140Hydrophobic
C17CD2LEU- 3794.330Hydrophobic
S32CBALA- 3894.410Hydrophobic
C27CBALA- 3893.660Hydrophobic
C27CG2VAL- 4194.220Hydrophobic
C28CGPHE- 4353.260Hydrophobic
C28CBPHE- 4353.280Hydrophobic
C17CZPHE- 4373.520Hydrophobic
C19CZPHE- 4374.190Hydrophobic
N23OMET- 4382.7135.53H-Bond
(Ligand Donor)
N25NMET- 4382.97167.87H-Bond
(Protein Donor)
C27CGMET- 4384.370Hydrophobic
C8SGCYS- 4423.770Hydrophobic
S32CD2LEU- 4893.760Hydrophobic
C27CD1LEU- 4893.720Hydrophobic