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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:

3ad6

2.150 Å

X-ray

2010-01-14

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Tyrosine-protein kinase Lck
ID:LCK_HUMAN
AC:P06239
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.10.2


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:3.566
Number of residues:27
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.812469.125

% Hydrophobic% Polar
52.5247.48
According to VolSite

Ligand :
3ad6_1 Structure
HET Code: KSC
Formula: C19H22N6O2
Molecular weight: 366.417 g/mol
DrugBank ID: -
Buried Surface Area:37.21 %
Polar Surface area: 106.57 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 3
Rings: 4
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 7

Mass center Coordinates

XYZ
27.341235.45168.19826


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
C21CBLEU- 2514.310Hydrophobic
C19CD2LEU- 2513.960Hydrophobic
C17CD1LEU- 2513.790Hydrophobic
C10CG1VAL- 2594.490Hydrophobic
N25OGLU- 3173.43134.62H-Bond
(Ligand Donor)
O24NMET- 3193.01153.56H-Bond
(Protein Donor)
C13CBSER- 3234.080Hydrophobic
C15CD2LEU- 37140Hydrophobic