scPDB - 2zv9 entry

Protein Data Bank Entry:

PDB ID : 2zv9

Resolution :2.760 Å

Experimental Method : X-ray

Deposition Date : 2008-11-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tyrosine-protein kinase Lyn
ID:	LYN_MOUSE
AC:	P25911
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	2.7.10.2

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	8.857
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.145	408.375

% Hydrophobic	% Polar
64.46	35.54
According to VolSite

Ligand :

HET Code:	PP2
Formula:	C15H16ClN5
Molecular weight:	301.774 g/mol
DrugBank ID:	DB03023
Buried Surface Area:	64.41 %
Polar Surface area:	69.62 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
19.7574	8.68824	-8.54214

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
C24	CB	LEU- 253	3.63	0	Hydrophobic	false
C6	CG1	VAL- 261	4.06	0	Hydrophobic	false
C24	CG1	VAL- 261	4.2	0	Hydrophobic	false
C25	CG2	VAL- 261	4.37	0	Hydrophobic	false
C12	CG1	VAL- 261	4.02	0	Hydrophobic	false
C6	CB	ALA- 273	4.32	0	Hydrophobic	false
C12	CB	ALA- 273	4.34	0	Hydrophobic	false
C13	CB	LYS- 275	3.79	0	Hydrophobic	false
C14	CD	LYS- 275	3.95	0	Hydrophobic	false
CL	CG	GLU- 290	4.32	0	Hydrophobic	false
CL	CE	MET- 294	3.21	0	Hydrophobic	false
CL	CG2	ILE- 317	3.66	0	Hydrophobic	false
CL	CG2	THR- 319	3.54	0	Hydrophobic	false
C13	CG2	THR- 319	3.67	0	Hydrophobic	false
N25	O	GLU- 320	3.2	167.2	H-Bond (Ligand Donor)	false
N4	N	MET- 322	3.15	157.36	H-Bond (Protein Donor)	false
C23	CB	SER- 326	4.07	0	Hydrophobic	false
C6	CG	LEU- 374	4.17	0	Hydrophobic	false
C16	CD2	LEU- 374	4.03	0	Hydrophobic	false
C16	CB	ALA- 384	4.06	0	Hydrophobic	false