scPDB - 2w5b entry

Protein Data Bank Entry:

PDB ID : 2w5b

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2008-12-08

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:	22.690
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.920	408.375

% Hydrophobic	% Polar
65.29	34.71
According to VolSite

Ligand :

HET Code:	AGS
Formula:	C10H14N5O12P3S
Molecular weight:	521.231 g/mol
DrugBank ID:	DB02930
Buried Surface Area:	54.99 %
Polar Surface area:	329.24 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
26.5062	12.8686	-16.1205

Binding mode :

What is Poseview ?

2D View
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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
C4'	CG2	ILE- 14	4.13	0	Hydrophobic	false
C1'	CG2	ILE- 14	3.71	0	Hydrophobic	false
C1'	SG	CYS- 22	4.48	0	Hydrophobic	false
C5'	CB	CYS- 22	3.89	0	Hydrophobic	false
O2A	NZ	LYS- 37	2.78	143.12	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 37	2.78	0	Ionic (Protein Cationic)	false
N6	O	GLU- 87	2.8	154.36	H-Bond (Ligand Donor)	false
N1	N	CYS- 89	2.86	163.77	H-Bond (Protein Donor)	false
C2'	CE2	PHE- 148	3.92	0	Hydrophobic	false
O2G	MG	MG- 1282	2.7	0	Metal Acceptor	false
O3A	MG	MG- 1282	2.54	0	Metal Acceptor	false