scPDB - 2xk4 entry

Protein Data Bank Entry:

PDB ID : 2xk4

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2010-07-07

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:	34.798
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.097	452.250

% Hydrophobic	% Polar
64.93	35.07
According to VolSite

Ligand :

HET Code:	OL2
Formula:	C22H22N3O6
Molecular weight:	424.427 g/mol
DrugBank ID:	-
Buried Surface Area:	57.99 %
Polar Surface area:	128.85 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	1
Rings:	3
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-25.8723	20.4907	-18.765

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	CG2	ILE- 14	3.68	0	Hydrophobic	false
C01	CB	CYS- 22	4.49	0	Hydrophobic	false
C05	SG	CYS- 22	4.11	0	Hydrophobic	false
C04	CD	LYS- 37	4.29	0	Hydrophobic	false
C01	CD	LYS- 37	3.86	0	Hydrophobic	false
O30	NZ	LYS- 37	3.17	161.82	H-Bond (Protein Donor)	false
O30	NZ	LYS- 37	3.17	0	Ionic (Protein Cationic)	false
C27	CG2	VAL- 68	4.02	0	Hydrophobic	false
C27	SD	MET- 86	3.77	0	Hydrophobic	false
N25	O	GLU- 87	2.67	167.01	H-Bond (Ligand Donor)	false
N23	N	CYS- 89	2.93	163.6	H-Bond (Protein Donor)	false
C14	CB	ASP- 93	4.46	0	Hydrophobic	false
C17	CB	SER- 96	4.2	0	Hydrophobic	false
DuAr	DuAr	PHE- 148	3.88	0	Aromatic Face/Face	false
O31	N	ASP- 159	2.67	164.65	H-Bond (Protein Donor)	false
C02	CZ	PHE- 160	3.52	0	Hydrophobic	false