scPDB - 2xkd entry

Protein Data Bank Entry:

PDB ID : 2xkd

Resolution :1.960 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:	33.478
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.893	378.000

% Hydrophobic	% Polar
61.61	38.39
According to VolSite

Ligand :

HET Code:	T3M
Formula:	C20H18N3O5
Molecular weight:	380.374 g/mol
DrugBank ID:	-
Buried Surface Area:	59.95 %
Polar Surface area:	119.62 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	1
Rings:	3
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
25.5887	-8.64425	18.8938

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
C8	CG2	ILE- 14	3.74	0	Hydrophobic	false
C22	SG	CYS- 22	3.63	0	Hydrophobic	false
O26	NZ	LYS- 37	2.76	131.37	H-Bond (Protein Donor)	false
O26	NZ	LYS- 37	2.76	0	Ionic (Protein Cationic)	false
O25	NZ	LYS- 37	3.7	0	Ionic (Protein Cationic)	false
C27	CG1	VAL- 68	4.44	0	Hydrophobic	false
C28	CG2	VAL- 68	4.27	0	Hydrophobic	false
O25	OH	TYR- 70	2.67	175.05	H-Bond (Protein Donor)	false
C27	SD	MET- 86	3.58	0	Hydrophobic	false
N18	O	GLU- 87	2.75	159.33	H-Bond (Ligand Donor)	false
C1	CE1	TYR- 88	4.09	0	Hydrophobic	false
N16	N	CYS- 89	2.89	167.01	H-Bond (Protein Donor)	false
C7	CB	SER- 96	4.11	0	Hydrophobic	false
C28	CZ	PHE- 148	3.39	0	Hydrophobic	false
O25	N	ASP- 159	2.88	129.93	H-Bond (Protein Donor)	false