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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:

4ezk

2.800 Å

X-ray

2012-05-02

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
ID:PK3CG_HUMAN
AC:P48736
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.1.153


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:94.787
Number of residues:32
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.991651.375

% Hydrophobic% Polar
56.4843.52
According to VolSite

Ligand :
4ezk_1 Structure
HET Code: 0SD
Formula: C27H34N7O2
Molecular weight: 488.605 g/mol
DrugBank ID: -
Buried Surface Area:53.2 %
Polar Surface area: 104.49 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 3
Rings: 6
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
18.7915-4.3425620.2345


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
CCGMET- 8044.480Hydrophobic
C3CGMET- 8044.230Hydrophobic
C11SDMET- 8044.450Hydrophobic
CCBALA- 8054.060Hydrophobic
C7CZ3TRP- 8123.610Hydrophobic
C26CZ3TRP- 8124.060Hydrophobic
C23CD1ILE- 8314.370Hydrophobic
C26CD1ILE- 8313.960Hydrophobic
C18CDLYS- 8334.220Hydrophobic
N4OHTYR- 8672.9128.49H-Bond
(Protein Donor)
C23CG2ILE- 8794.120Hydrophobic
C20CD1ILE- 8793.80Hydrophobic
C25CG2ILE- 8814.060Hydrophobic
C24CG2VAL- 8823.750Hydrophobic
C25CBVAL- 8824.360Hydrophobic
C25CBALA- 8854.430Hydrophobic
C4CDLYS- 8904.440Hydrophobic
C25CEMET- 9534.190Hydrophobic
C26SDMET- 9534.40Hydrophobic
C24CE2PHE- 9613.950Hydrophobic
C16CD1ILE- 9633.90Hydrophobic
N4NASP- 9643.21149.16H-Bond
(Protein Donor)
C20CBASP- 9643.610Hydrophobic