scPDB - 4afe entry

Protein Data Bank Entry:

PDB ID : 4afe

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2012-01-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Serine/threonine-protein kinase Nek2
ID:	NEK2_HUMAN
AC:	P51955
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.1

Chains:

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

Ligand binding site composition:

B-Factor:	36.212
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.949	475.875

% Hydrophobic	% Polar
63.83	36.17
According to VolSite

Ligand :

HET Code:	GGY
Formula:	C24H26F3N4O2S
Molecular weight:	491.549 g/mol
DrugBank ID:	-
Buried Surface Area:	58.85 %
Polar Surface area:	123.91 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
1.81038	-9.31668	11.188

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
F07	CG2	ILE- 14	4.26	0	Hydrophobic	false
C15	CD1	ILE- 14	4.18	0	Hydrophobic	false
S24	CG2	ILE- 14	3.44	0	Hydrophobic	false
C01	CZ	TYR- 19	3.42	0	Hydrophobic	false
F08	CZ	TYR- 19	3.77	0	Hydrophobic	false
C01	CB	CYS- 22	3.89	0	Hydrophobic	false
C02	SG	CYS- 22	3.81	0	Hydrophobic	false
F07	SG	CYS- 22	3.79	0	Hydrophobic	false
F08	CB	CYS- 22	3.73	0	Hydrophobic	false
C11	SG	CYS- 22	3.96	0	Hydrophobic	false
C13	CG2	VAL- 35	4.43	0	Hydrophobic	false
C29	CG1	VAL- 68	4.15	0	Hydrophobic	false
C29	SD	MET- 86	3.74	0	Hydrophobic	false
N28	O	GLU- 87	2.59	176.04	H-Bond (Ligand Donor)	false
C15	CB	CYS- 89	4.42	0	Hydrophobic	false
N26	N	CYS- 89	2.77	163.57	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 148	3.99	0	Aromatic Face/Face	false
N33	OD1	ASP- 159	3.4	137.49	H-Bond (Ligand Donor)	false
O34	N	ASP- 159	3.09	155.08	H-Bond (Protein Donor)	false