scPDB - 3vf8 entry

Protein Data Bank Entry:

PDB ID : 3vf8

Resolution :2.080 Å

Experimental Method : X-ray

Deposition Date : 2012-01-09

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 SYK
ID:	KSYK_HUMAN
AC:	P43405
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:	33.946
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.271	435.375

% Hydrophobic	% Polar
55.81	44.19
According to VolSite

Ligand :

HET Code:	0JE
Formula:	C17H21FN6O2
Molecular weight:	360.386 g/mol
DrugBank ID:	-
Buried Surface Area:	55.31 %
Polar Surface area:	98.93 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-1.14162	-0.242538	-14.7942

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
CAD	CB	LEU- 377	3.56	0	Hydrophobic	false
CAC	CD2	LEU- 377	3.88	0	Hydrophobic	false
NAL	O	GLU- 449	2.98	159.17	H-Bond (Ligand Donor)	false
CAC	CE	MET- 450	3.92	0	Hydrophobic	false
NAE	O	ALA- 451	2.77	131.14	H-Bond (Ligand Donor)	false
NAK	N	ALA- 451	3.08	165.59	H-Bond (Protein Donor)	false
CAD	CG	PRO- 455	4.43	0	Hydrophobic	false
CAV	CG	PRO- 455	4.12	0	Hydrophobic	false
CAV	CD2	LEU- 501	4.32	0	Hydrophobic	false
OAR	OG	SER- 511	2.72	166.48	H-Bond (Protein Donor)	false
CAT	CB	SER- 511	4.31	0	Hydrophobic	false
CAT	CB	ASP- 512	3.61	0	Hydrophobic	false
OAR	O	HOH- 821	2.9	135.54	H-Bond (Protein Donor)	false