scPDB - 3ibe entry

Protein Data Bank Entry:

PDB ID : 3ibe

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2009-07-15

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:	65.602
Number of residues:	40
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.312	472.500

% Hydrophobic	% Polar
64.29	35.71
According to VolSite

Ligand :

HET Code:	L64
Formula:	C32H32N10O3
Molecular weight:	604.662 g/mol
DrugBank ID:	-
Buried Surface Area:	58.44 %
Polar Surface area:	143.28 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	2
Rings:	7
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
42.2616	15.8974	32.9107

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
C9	CE	MET- 804	3.75	0	Hydrophobic	false
C13	CE	MET- 804	3.85	0	Hydrophobic	false
C8	CB	SER- 806	4.4	0	Hydrophobic	false
C29	CZ3	TRP- 812	4.14	0	Hydrophobic	false
C13	CD1	ILE- 831	4.1	0	Hydrophobic	false
C29	CD1	ILE- 831	3.58	0	Hydrophobic	false
C32	CD1	ILE- 831	3.82	0	Hydrophobic	false
O2	NZ	LYS- 833	2.89	162.7	H-Bond (Protein Donor)	false
C25	CB	ASP- 836	3.63	0	Hydrophobic	false
C28	CB	ASP- 836	4.07	0	Hydrophobic	false
C28	CD2	LEU- 838	4.24	0	Hydrophobic	false
N7	OD2	ASP- 841	3.2	145.42	H-Bond (Ligand Donor)	false
N8	OD1	ASP- 841	2.85	133.93	H-Bond (Ligand Donor)	false
C31	CG	TYR- 867	4.44	0	Hydrophobic	false
C32	CG2	ILE- 879	3.84	0	Hydrophobic	false
C21	CD1	ILE- 879	3.25	0	Hydrophobic	false
C29	CG1	ILE- 881	4.04	0	Hydrophobic	false
C30	CG2	ILE- 881	4.28	0	Hydrophobic	false
O3	N	VAL- 882	2.65	174.96	H-Bond (Protein Donor)	false
C30	CB	VAL- 882	4.27	0	Hydrophobic	false
C31	CG2	VAL- 882	3.94	0	Hydrophobic	false
C10	CG2	THR- 887	4.02	0	Hydrophobic	false
C13	SD	MET- 953	4.01	0	Hydrophobic	false
C30	CE	MET- 953	3.75	0	Hydrophobic	false
C31	CE1	PHE- 961	4.33	0	Hydrophobic	false
C13	CD1	ILE- 963	4.09	0	Hydrophobic	false
C17	CB	ILE- 963	4.37	0	Hydrophobic	false
C32	CG2	ILE- 963	4.19	0	Hydrophobic	false
C19	CB	ASP- 964	3.2	0	Hydrophobic	false