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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:

4id7

3.000 Å

X-ray

2012-12-11

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Activated CDC42 kinase 1
ID:ACK1_HUMAN
AC:Q07912
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:85.340
Number of residues:32
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.4521346.625

% Hydrophobic% Polar
52.6347.37
According to VolSite

Ligand :
4id7_1 Structure
HET Code: 1G0
Formula: C22H20N4O2
Molecular weight: 372.420 g/mol
DrugBank ID: -
Buried Surface Area:59.38 %
Polar Surface area: 85.67 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 2
Rings: 5
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
33.14089.7441428.5463


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
C5CG1VAL- 1404.320Hydrophobic
C30CG1VAL- 1404.210Hydrophobic
C21CDLYS- 1583.430Hydrophobic
C26CGMET- 1813.530Hydrophobic
C27CG2ILE- 1903.870Hydrophobic
C25CD2LEU- 1923.990Hydrophobic
C26CBLEU- 1923.940Hydrophobic
C24SDMET- 2033.760Hydrophobic
C29CG2THR- 2053.650Hydrophobic
C23CG2THR- 2053.590Hydrophobic
N13OGLU- 2063.02155.79H-Bond
(Ligand Donor)
N14NALA- 2083.23156.82H-Bond
(Protein Donor)
C7CD2LEU- 2594.040Hydrophobic