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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:

3ml9

2.550 Å

X-ray

2010-04-16

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:49.993
Number of residues:33
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.653874.125

% Hydrophobic% Polar
40.5459.46
According to VolSite

Ligand :
3ml9_1 Structure
HET Code: ML9
Formula: C22H27N5O4
Molecular weight: 425.481 g/mol
DrugBank ID: DB11974
Buried Surface Area:58.31 %
Polar Surface area: 123.69 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 2
Rings: 4
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
45.046515.695531.3265


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
C26SDMET- 8043.760Hydrophobic
C27CZ3TRP- 8123.730Hydrophobic
C5CD1ILE- 8314.370Hydrophobic
C27CD1ILE- 8313.920Hydrophobic
C14CD1ILE- 8314.090Hydrophobic
C20CD1LEU- 8384.270Hydrophobic
C20CBASP- 8414.470Hydrophobic
C21CGTYR- 8673.480Hydrophobic
C21CG2ILE- 8794.310Hydrophobic
C20CD1ILE- 8794.130Hydrophobic
C15CD1ILE- 8793.550Hydrophobic
C21CG2VAL- 8823.540Hydrophobic
N1NVAL- 8822.82162.26H-Bond
(Protein Donor)
N12OVAL- 8822.6137.78H-Bond
(Ligand Donor)
O31NZLYS- 8903.19129.58H-Bond
(Protein Donor)
C5SDMET- 9534.090Hydrophobic
C23SDMET- 9534.020Hydrophobic
C21CE1PHE- 9614.140Hydrophobic
C5CG2ILE- 9634.260Hydrophobic
C23CD1ILE- 9634.230Hydrophobic
C20CBASP- 9644.420Hydrophobic