scPDB - 2xnn entry

Protein Data Bank Entry:

PDB ID : 2xnn

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2010-08-05

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:	32.518
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.502	1090.125

% Hydrophobic	% Polar
57.59	42.41
According to VolSite

Ligand :

HET Code:	430
Formula:	C21H16F3N3O2S
Molecular weight:	431.431 g/mol
DrugBank ID:	-
Buried Surface Area:	54.42 %
Polar Surface area:	98.38 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	1
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
25.4063	9.75467	-17.036

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
C13	CG2	ILE- 14	3.83	0	Hydrophobic	false
F28	CG2	ILE- 14	3.45	0	Hydrophobic	false
F29	SG	CYS- 22	3.23	0	Hydrophobic	false
F30	CB	CYS- 22	3.73	0	Hydrophobic	false
DuAr	NZ	LYS- 37	2.83	162.6	Pi/Cation	false
S16	SD	MET- 86	4.24	0	Hydrophobic	false
N09	N	CYS- 89	2.77	169.62	H-Bond (Protein Donor)	false
C24	CB	ASP- 93	3.7	0	Hydrophobic	false
C23	CZ	PHE- 148	3.45	0	Hydrophobic	false
N19	OD2	ASP- 159	3.32	164.62	H-Bond (Ligand Donor)	false
N19	O	ASP- 159	3.12	125.11	H-Bond (Ligand Donor)	false
O20	N	ASP- 159	3.4	127.59	H-Bond (Protein Donor)	false