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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:

3ac3

2.550 Å

X-ray

2009-12-28

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:5.820
Number of residues:27
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.234472.500

% Hydrophobic% Polar
57.8642.14
According to VolSite

Ligand :
3ac3_1 Structure
HET Code: KSH
Formula: C22H28N6O4
Molecular weight: 440.496 g/mol
DrugBank ID: -
Buried Surface Area:37.91 %
Polar Surface area: 127.24 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 3
Rings: 4
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 8

Mass center Coordinates

XYZ
7.110841.31637-8.25541


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
C19CD2LEU- 2514.480Hydrophobic
C32CD2LEU- 2514.40Hydrophobic
C18CD1LEU- 2513.60Hydrophobic
O11NMET- 3192.77141.8H-Bond
(Protein Donor)
C53CBSER- 3233.680Hydrophobic