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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:

2v7a

2.500 Å

X-ray

2007-07-27

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Tyrosine-protein kinase ABL1
ID:ABL1_HUMAN
AC:P00519
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:21.373
Number of residues:36
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.865739.125

% Hydrophobic% Polar
43.3856.62
According to VolSite

Ligand :
2v7a_1 Structure
HET Code: 627
Formula: C26H31N6O3
Molecular weight: 475.563 g/mol
DrugBank ID: DB11778
Buried Surface Area:52.86 %
Polar Surface area: 95 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 3
Rings: 5
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-42.4158-50.6965-10.8478


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
C7CD2LEU- 2484.070Hydrophobic
C36CG2VAL- 2564.470Hydrophobic
O26NZLYS- 2713.29128.83H-Bond
(Protein Donor)
N2OGLU- 3162.83149.16H-Bond
(Ligand Donor)
N4NMET- 3182.89170.65H-Bond
(Protein Donor)
N5OMET- 3183.27169.58H-Bond
(Ligand Donor)
C31CBASN- 3224.180Hydrophobic
C33CD2LEU- 3703.90Hydrophobic
C35CD1LEU- 3703.640Hydrophobic
C33CBALA- 3803.980Hydrophobic
C29CBASP- 3814.160Hydrophobic