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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:

4ezj

2.670 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:56.612
Number of residues:33
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.077695.250

% Hydrophobic% Polar
57.2842.72
According to VolSite

Ligand :
4ezj_1 Structure
HET Code: 0SC
Formula: C28H34FN6O2
Molecular weight: 505.607 g/mol
DrugBank ID: -
Buried Surface Area:49.3 %
Polar Surface area: 91.6 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 3
Rings: 6
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 5

Mass center Coordinates

XYZ
18.6424-5.5331419.6412


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
C12CEMET- 8043.360Hydrophobic
C28CZ3TRP- 8124.210Hydrophobic
C8CZ3TRP- 8123.250Hydrophobic
C3CD2TRP- 8124.280Hydrophobic
C28CD1ILE- 8313.790Hydrophobic
C25CD1ILE- 8313.810Hydrophobic
C23CDLYS- 8333.850Hydrophobic
C22CD1LEU- 8384.490Hydrophobic
N5OD2ASP- 8412.79151.46H-Bond
(Ligand Donor)
C25CG2ILE- 8793.80Hydrophobic
C21CD1ILE- 8793.680Hydrophobic
C27CG2ILE- 8814.280Hydrophobic
C27CBVAL- 8824.290Hydrophobic
C26CG2VAL- 8823.940Hydrophobic
O1NVAL- 8822.58170.48H-Bond
(Protein Donor)
C11CG2THR- 8874.120Hydrophobic
C28SDMET- 9534.130Hydrophobic
C27CEMET- 9533.920Hydrophobic
C26CE2PHE- 9613.920Hydrophobic
C18CBILE- 9634.240Hydrophobic
C12CD1ILE- 9633.730Hydrophobic
C25CG2ILE- 9634.210Hydrophobic
C21CBASP- 9644.490Hydrophobic