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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:

4j6i

2.900 Å

X-ray

2013-02-11

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:79.205
Number of residues:33
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.393587.250

% Hydrophobic% Polar
49.4350.57
According to VolSite

Ligand :
4j6i_1 Structure
HET Code: 1JV
Formula: C22H21F3N6O2S
Molecular weight: 490.501 g/mol
DrugBank ID: -
Buried Surface Area:59.8 %
Polar Surface area: 119.12 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 1
Rings: 5
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
19.524261.645122.0963


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
F31SDMET- 8044.250Hydrophobic
F32SDMET- 8043.90Hydrophobic
F33CGPRO- 8103.910Hydrophobic
C1CZ2TRP- 8123.960Hydrophobic
C3CH2TRP- 8123.540Hydrophobic
F31CD1ILE- 8313.260Hydrophobic
C14CD1ILE- 8313.80Hydrophobic
C30CDLYS- 8334.230Hydrophobic
C18CGTYR- 8673.940Hydrophobic
S23CZTYR- 8673.340Hydrophobic
C18CG2ILE- 8794.430Hydrophobic
S23CG2ILE- 8793.560Hydrophobic
F31CD1ILE- 8794.460Hydrophobic
C3CG2ILE- 8813.680Hydrophobic
C34CG2ILE- 8813.730Hydrophobic
O16NVAL- 8822.94156.06H-Bond
(Protein Donor)
C17CBVAL- 8823.660Hydrophobic
C18CG2VAL- 8824.230Hydrophobic
C3CDLYS- 8833.740Hydrophobic
O4NASP- 8842.8147.31H-Bond
(Protein Donor)
C14SDMET- 9533.990Hydrophobic
C17SDMET- 9534.050Hydrophobic
C12CEMET- 9533.960Hydrophobic
C17CE1PHE- 9613.840Hydrophobic
C18CG2ILE- 9634.040Hydrophobic
S23CG2ILE- 9633.490Hydrophobic
C29CD1ILE- 9634.450Hydrophobic