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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:

3v5j

2.590 Å

X-ray

2011-12-16

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
B100 %


Ligand binding site composition:

B-Factor:42.194
Number of residues:25
Including
Standard Amino Acids: 25
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.097560.250

% Hydrophobic% Polar
47.5952.41
According to VolSite

Ligand :
3v5j_2 Structure
HET Code: 0F2
Formula: C24H31N4O3S
Molecular weight: 455.593 g/mol
DrugBank ID: -
Buried Surface Area:44.6 %
Polar Surface area: 96.44 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 4
Rings: 5
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-42.786111.819625.0841


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
CBCCG2ILE- 3694.250Hydrophobic
CAECD1ILE- 3693.520Hydrophobic
CAQCG2VAL- 3773.70Hydrophobic
S1CG1VAL- 3774.020Hydrophobic
NAVOGLU- 4362.79140.63H-Bond
(Ligand Donor)
CBCCZPHE- 4374.090Hydrophobic
CACCZPHE- 4373.410Hydrophobic
NAGOMET- 4382.82129.47H-Bond
(Ligand Donor)
NAUNMET- 4383.07147.42H-Bond
(Protein Donor)
S1CD2LEU- 4893.970Hydrophobic