scPDB - 3vs5 entry

Protein Data Bank Entry:

PDB ID : 3vs5

Resolution :2.850 Å

Experimental Method : X-ray

Deposition Date : 2012-04-21

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 HCK
ID:	HCK_HUMAN
AC:	P08631
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.10.2

Chains:

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

Ligand binding site composition:

B-Factor:	42.504
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.526	1059.750

% Hydrophobic	% Polar
58.92	41.08
According to VolSite

Ligand :

HET Code:	VSG
Formula:	C24H26N5O
Molecular weight:	400.496 g/mol
DrugBank ID:	-
Buried Surface Area:	65.64 %
Polar Surface area:	70.4 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:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
-5.18303	-0.454067	17.4135

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
CAR	CB	LEU- 273	3.64	0	Hydrophobic	false
CAR	CG1	VAL- 281	4.02	0	Hydrophobic	false
C5	CG1	VAL- 281	4.25	0	Hydrophobic	false
CAJ	CG1	VAL- 281	4.17	0	Hydrophobic	false
C5	CB	ALA- 293	4.38	0	Hydrophobic	false
CAP	CB	ALA- 293	4.25	0	Hydrophobic	false
CAO	CB	LYS- 295	4.38	0	Hydrophobic	false
CAM	CD	LYS- 295	3.81	0	Hydrophobic	false
CBA	SD	MET- 314	4.04	0	Hydrophobic	false
CBD	CG1	VAL- 323	3.35	0	Hydrophobic	false
CAZ	CG2	ILE- 336	3.9	0	Hydrophobic	false
CAO	CG2	THR- 338	3.42	0	Hydrophobic	false
CBD	CG2	THR- 338	4.01	0	Hydrophobic	false
NAK	O	GLU- 339	3.05	162.87	H-Bond (Ligand Donor)	false
N1	N	MET- 341	2.88	156.73	H-Bond (Protein Donor)	false
CAV	CB	SER- 345	3.88	0	Hydrophobic	false
CAV	CD2	LEU- 393	4.06	0	Hydrophobic	false
C5	CD1	LEU- 393	3.58	0	Hydrophobic	false
CAJ	CD1	LEU- 393	3.88	0	Hydrophobic	false
CBD	CB	ALA- 403	4.15	0	Hydrophobic	false
CAM	CB	ALA- 403	3.91	0	Hydrophobic	false
CBA	CD1	LEU- 407	3.6	0	Hydrophobic	false