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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:

4d4s

2.000 Å

X-ray

2014-10-31

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Focal adhesion kinase 1
ID:FAK1_CHICK
AC:Q00944
Organism:Gallus gallus
Reign:Eukaryota
TaxID:9031
EC Number:2.7.10.2


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:42.624
Number of residues:30
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.289482.625

% Hydrophobic% Polar
60.1439.86
According to VolSite

Ligand :
4d4s_1 Structure
HET Code: BI9
Formula: C23H25ClN6O3
Molecular weight: 468.936 g/mol
DrugBank ID: DB07460
Buried Surface Area:57.9 %
Polar Surface area: 100.64 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: 7

Mass center Coordinates

XYZ
18.438513.789427.0037


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
CBDCBILE- 4284.330Hydrophobic
CALCD1ILE- 4283.650Hydrophobic
CAQCG1ILE- 4284.040Hydrophobic
CBACBILE- 4284.050Hydrophobic
CAWCBVAL- 4364.360Hydrophobic
CAPCG2VAL- 4364.490Hydrophobic
CAQCG1VAL- 4363.630Hydrophobic
CAUCGGLN- 4384.160Hydrophobic
C5CBALA- 4523.680Hydrophobic
OAINZLYS- 4543.02147.73H-Bond
(Protein Donor)
C5CEMET- 4993.880Hydrophobic
CL5SDMET- 4994.150Hydrophobic
CAUCD1LEU- 5014.030Hydrophobic
NAHOCYS- 5022.75134.17H-Bond
(Ligand Donor)
N1NCYS- 5022.94161.08H-Bond
(Protein Donor)
CAXCGGLU- 5064.060Hydrophobic
CAZCGGLU- 5063.860Hydrophobic
C5CGLEU- 5534.320Hydrophobic
CL5CD1LEU- 5533.450Hydrophobic
CAJCD2LEU- 5534.190Hydrophobic