scPDB - 2xno entry

Protein Data Bank Entry:

PDB ID : 2xno

Resolution :1.980 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:	28.675
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.486	330.750

% Hydrophobic	% Polar
57.14	42.86
According to VolSite

Ligand :

HET Code:	ED8
Formula:	C26H26F3N4O3S
Molecular weight:	531.570 g/mol
DrugBank ID:	-
Buried Surface Area:	52.49 %
Polar Surface area:	112.05 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-26.1413	10.1448	18.0643

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
C09	CD1	ILE- 14	4.25	0	Hydrophobic	false
F26	CG2	ILE- 14	3.8	0	Hydrophobic	false
F27	CG2	ILE- 14	4.04	0	Hydrophobic	false
C36	CG2	ILE- 14	3.28	0	Hydrophobic	false
C07	CG2	ILE- 14	3.86	0	Hydrophobic	false
F26	CB	CYS- 22	3.36	0	Hydrophobic	false
O17	NZ	LYS- 37	3.16	128.87	H-Bond (Protein Donor)	false
DuAr	NZ	LYS- 37	3.54	41.79	Pi/Cation	false
S33	CG1	VAL- 68	4.1	0	Hydrophobic	false
S33	SD	MET- 86	3.86	0	Hydrophobic	false
N11	N	CYS- 89	2.61	171.31	H-Bond (Protein Donor)	false
C04	CB	ASP- 93	4.48	0	Hydrophobic	false
C22	CB	ASP- 93	4.2	0	Hydrophobic	false
C20	CZ	PHE- 148	3.35	0	Hydrophobic	false
C35	CE2	PHE- 148	3.48	0	Hydrophobic	false
N31	OD1	ASP- 159	3.25	136.26	H-Bond (Ligand Donor)	false
N31	O	ASP- 159	2.92	130.4	H-Bond (Ligand Donor)	false
O32	N	ASP- 159	3.33	134.44	H-Bond (Protein Donor)	false