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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:

2v4l

2.500 Å

X-ray

2008-09-25

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:19.577
Number of residues:26
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.503668.250

% Hydrophobic% Polar
44.9555.05
According to VolSite

Ligand :
2v4l_1 Structure
HET Code: ABJ
Formula: C14H15N5O
Molecular weight: 269.302 g/mol
DrugBank ID: DB07335
Buried Surface Area:54.78 %
Polar Surface area: 89.85 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 2
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
45.077813.144131.4757


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
C20CZ3TRP- 8123.820Hydrophobic
C4CD1ILE- 8313.620Hydrophobic
C28CD1ILE- 8313.840Hydrophobic
O33NZLYS- 8333.27141.2H-Bond
(Protein Donor)
C30CG2ILE- 8794.040Hydrophobic
C26CD1ILE- 8793.580Hydrophobic
N1OGLU- 8803.04149.17H-Bond
(Ligand Donor)
N5NVAL- 8823.1166.59H-Bond
(Protein Donor)
C4SDMET- 9533.880Hydrophobic
C14CEMET- 9533.60Hydrophobic
C18CD1ILE- 9633.670Hydrophobic
C27CBILE- 9633.560Hydrophobic
C26CBASP- 9644.150Hydrophobic