scPDB - 3vrz entry

Protein Data Bank Entry:

PDB ID : 3vrz

Resolution :2.220 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:	42.260
Number of residues:	40
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.387	1353.375

% Hydrophobic	% Polar
54.36	45.64
According to VolSite

Ligand :

HET Code:	VRZ
Formula:	C25H26N6O
Molecular weight:	426.514 g/mol
DrugBank ID:	-
Buried Surface Area:	64.74 %
Polar Surface area:	97.86 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
4.18691	2.95006	-10.2867

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
CAP	CB	LEU- 273	3.69	0	Hydrophobic	false
C5	CG1	VAL- 281	4.15	0	Hydrophobic	false
CAP	CG1	VAL- 281	3.69	0	Hydrophobic	false
CAZ	CG2	VAL- 281	4.27	0	Hydrophobic	false
C5	CB	ALA- 293	4.11	0	Hydrophobic	false
CAH	CB	LYS- 295	4.11	0	Hydrophobic	false
CAE	CZ	PHE- 307	3.47	0	Hydrophobic	false
CAD	CG	MET- 314	3.63	0	Hydrophobic	false
CAF	CD2	LEU- 325	4.28	0	Hydrophobic	false
CAX	CG2	ILE- 336	4.49	0	Hydrophobic	false
CAE	CD1	ILE- 336	4.41	0	Hydrophobic	false
CAG	CG1	ILE- 336	3.99	0	Hydrophobic	false
CAH	CG2	THR- 338	3.96	0	Hydrophobic	false
NAA	O	GLU- 339	3.06	172.52	H-Bond (Ligand Donor)	false
N1	N	MET- 341	2.9	169.93	H-Bond (Protein Donor)	false
CAQ	CB	SER- 345	4.11	0	Hydrophobic	false
CAQ	CD2	LEU- 393	3.91	0	Hydrophobic	false
C5	CD1	LEU- 393	3.5	0	Hydrophobic	false
CAZ	CD1	LEU- 393	3.76	0	Hydrophobic	false
CAI	CB	ALA- 403	3.75	0	Hydrophobic	false
NAV	OD1	ASP- 404	2.85	165.92	H-Bond (Ligand Donor)	false
NAU	OD1	ASP- 404	3.3	135.17	H-Bond (Ligand Donor)	false
CAG	CD1	LEU- 407	4.25	0	Hydrophobic	false
CAC	CB	VAL- 410	4.41	0	Hydrophobic	false