Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3l08

2.700 Å

X-ray

2009-12-09

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:66.569
Number of residues:36
Including
Standard Amino Acids: 36
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.035786.375

% Hydrophobic% Polar
54.5145.49
According to VolSite

Ligand :
3l08_1 Structure
HET Code: ZIG
Formula: C25H17F2N5O3S
Molecular weight: 505.496 g/mol
DrugBank ID: DB12703
Buried Surface Area:64.58 %
Polar Surface area: 115.33 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 1
Rings: 5
Aromatic rings: 5
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
24.92315.618121.3066


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
F35CEMET- 8043.340Hydrophobic
C6CEMET- 8043.440Hydrophobic
C10CD1ILE- 8313.60Hydrophobic
C12CD1ILE- 8313.870Hydrophobic
C10CD1ILE- 8313.60Hydrophobic
C1CDLYS- 8334.330Hydrophobic
C23CDLYS- 8334.430Hydrophobic
C1CD2LEU- 8383.720Hydrophobic
C1CD1ILE- 8793.860Hydrophobic
C2CG2ILE- 8793.310Hydrophobic
C23CD1ILE- 8794.110Hydrophobic
C2CG2ILE- 8793.310Hydrophobic
C7CG2ILE- 8814.250Hydrophobic
N26NVAL- 8822.9158.87H-Bond
(Protein Donor)
C7CEMET- 9533.410Hydrophobic
C22SDMET- 9533.850Hydrophobic
C18SDMET- 9533.560Hydrophobic
C2CG2ILE- 9634.490Hydrophobic
C10CD1ILE- 9634.270Hydrophobic
C21CBILE- 9634.340Hydrophobic
C16CD1ILE- 9633.990Hydrophobic
C23CBASP- 9644.450Hydrophobic
C3CBASP- 9643.70Hydrophobic