scPDB - 4dk5 entry

Protein Data Bank Entry:

PDB ID : 4dk5

Resolution :2.950 Å

Experimental Method : X-ray

Deposition Date : 2012-02-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	8.100	8.250	8.250	0.150	8.400	2

List of CHEMBLId :

CHEMBL2165017

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:	70.449
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.762	722.250

% Hydrophobic	% Polar
56.07	43.93
According to VolSite

Ligand :

HET Code:	0KO
Formula:	C21H28N9O3S
Molecular weight:	486.571 g/mol
DrugBank ID:	-
Buried Surface Area:	59.11 %
Polar Surface area:	161.92 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	3
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
21.7389	15.8197	21.1048

Binding mode :

What is Poseview ?

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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
O34	NZ	LYS- 802	2.79	163.06	H-Bond (Protein Donor)	false
C29	CE	MET- 804	3.9	0	Hydrophobic	false
C14	CB	ALA- 805	3.84	0	Hydrophobic	false
C32	CB	ALA- 805	4.46	0	Hydrophobic	false
O33	N	ALA- 805	2.58	139.75	H-Bond (Protein Donor)	false
C12	CZ3	TRP- 812	4.44	0	Hydrophobic	false
C3	CD1	ILE- 831	4.24	0	Hydrophobic	false
C29	CD1	ILE- 831	4.04	0	Hydrophobic	false
O30	NZ	LYS- 833	3.45	163.33	H-Bond (Protein Donor)	false
C28	CD	LYS- 833	4.16	0	Hydrophobic	false
C31	CD2	LEU- 838	3.81	0	Hydrophobic	false
C22	CD1	TYR- 867	3.55	0	Hydrophobic	false
C22	CG2	ILE- 879	3.78	0	Hydrophobic	false
C22	CG2	VAL- 882	4.22	0	Hydrophobic	false
N19	N	VAL- 882	3.17	168.34	H-Bond (Protein Donor)	false
N23	O	VAL- 882	2.86	148.17	H-Bond (Ligand Donor)	false
C5	CG2	THR- 887	4.36	0	Hydrophobic	false
C4	SD	MET- 953	3.69	0	Hydrophobic	false
C24	CD1	ILE- 963	4.35	0	Hydrophobic	false
C22	CG2	ILE- 963	4.05	0	Hydrophobic	false
C3	CD1	ILE- 963	3.75	0	Hydrophobic	false
C31	CB	ASP- 964	4.43	0	Hydrophobic	false