scPDB - 4ajw entry

Protein Data Bank Entry:

PDB ID : 4ajw

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2012-02-20

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 delta isoform
ID:	PK3CD_MOUSE
AC:	O35904
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	2.7.1.153

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	63.724
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.083	722.250

% Hydrophobic	% Polar
59.35	40.65
According to VolSite

Ligand :

HET Code:	VWN
Formula:	C17H19N5O2
Molecular weight:	325.365 g/mol
DrugBank ID:	-
Buried Surface Area:	66.04 %
Polar Surface area:	71.75 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
10.9759	-6.22662	7.74896

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
C15	SD	MET- 752	4.12	0	Hydrophobic	false
C24	SD	MET- 752	4.2	0	Hydrophobic	false
C20	CB	MET- 752	3.59	0	Hydrophobic	false
C23	CG	PRO- 758	3.61	0	Hydrophobic	false
C6	CH2	TRP- 760	4.37	0	Hydrophobic	false
C22	CB	TRP- 760	3.56	0	Hydrophobic	false
C23	CG2	ILE- 777	3.7	0	Hydrophobic	false
C7	CD1	ILE- 777	3.95	0	Hydrophobic	false
C3	CZ	TYR- 813	3.82	0	Hydrophobic	false
C4	CD2	TYR- 813	4.1	0	Hydrophobic	false
C3	CG2	ILE- 825	4.16	0	Hydrophobic	false
C6	CG1	VAL- 827	4.2	0	Hydrophobic	false
C4	CG2	VAL- 828	3.72	0	Hydrophobic	false
O5	N	VAL- 828	2.94	167.45	H-Bond (Protein Donor)	false
C7	SD	MET- 900	3.55	0	Hydrophobic	false
C3	CG2	ILE- 910	3.76	0	Hydrophobic	false