scPDB - 3ml8 entry

Protein Data Bank Entry:

PDB ID : 3ml8

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2010-04-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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
A	100 %

Ligand binding site composition:

B-Factor:	53.320
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.042	597.375

% Hydrophobic	% Polar
57.63	42.37
According to VolSite

Ligand :

HET Code:	ML8
Formula:	C21H24N4O2
Molecular weight:	364.441 g/mol
DrugBank ID:	-
Buried Surface Area:	68.51 %
Polar Surface area:	78.35 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
44.7511	14.3281	30.5737

Binding mode :

What is Poseview ?

2D View
3D View

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

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C17	SD	MET- 804	3.84	0	Hydrophobic	false
C18	CE	MET- 804	4.02	0	Hydrophobic	false
C18	CZ3	TRP- 812	4.34	0	Hydrophobic	false
C19	CH2	TRP- 812	3.78	0	Hydrophobic	false
C1	CD1	ILE- 831	4.44	0	Hydrophobic	false
C18	CD1	ILE- 831	3.83	0	Hydrophobic	false
C23	CD1	LEU- 838	4.38	0	Hydrophobic	false
C26	CB	ASP- 841	3.68	0	Hydrophobic	false
C13	CG	TYR- 867	3.59	0	Hydrophobic	false
C26	CE1	TYR- 867	3.61	0	Hydrophobic	false
O27	OH	TYR- 867	2.54	142.53	H-Bond (Protein Donor)	false
C21	CG2	ILE- 879	3.71	0	Hydrophobic	false
C13	CG2	ILE- 879	4.3	0	Hydrophobic	false
C22	CD1	ILE- 879	3.78	0	Hydrophobic	false
C23	CD1	ILE- 879	3.78	0	Hydrophobic	false
C19	CG2	ILE- 881	3.64	0	Hydrophobic	false
C13	CG2	VAL- 882	3.59	0	Hydrophobic	false
N5	N	VAL- 882	2.9	139.58	H-Bond (Protein Donor)	false
C19	CB	ALA- 885	4.45	0	Hydrophobic	false
C1	SD	MET- 953	4.01	0	Hydrophobic	false
C15	SD	MET- 953	4.12	0	Hydrophobic	false
C8	CE	MET- 953	4.15	0	Hydrophobic	false
C19	CE	MET- 953	4.11	0	Hydrophobic	false
C13	CE1	PHE- 961	4.22	0	Hydrophobic	false
C15	CD1	ILE- 963	4.4	0	Hydrophobic	false
C21	CB	ILE- 963	4.2	0	Hydrophobic	false
O27	N	ASP- 964	2.9	125.34	H-Bond (Protein Donor)	false
C24	CB	ASP- 964	3.82	0	Hydrophobic	false