scPDB - 3vf9 entry

Protein Data Bank Entry:

PDB ID : 3vf9

Resolution :2.300 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:	47.050
Number of residues:	24
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.595	550.125

% Hydrophobic	% Polar
63.19	36.81
According to VolSite

Ligand :

HET Code:	477
Formula:	C19H19F2N3OS
Molecular weight:	375.435 g/mol
DrugBank ID:	-
Buried Surface Area:	51.8 %
Polar Surface area:	92.94 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	3
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-0.990571	-1.36124	-15.3847

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
CAW	CD2	LEU- 377	3.74	0	Hydrophobic	false
CAL	CB	LEU- 377	3.73	0	Hydrophobic	false
CAI	CD2	LEU- 377	3.62	0	Hydrophobic	false
SAO	CG1	VAL- 385	4.14	0	Hydrophobic	false
SAO	CB	ALA- 400	4.48	0	Hydrophobic	false
NAA	O	GLU- 449	2.8	149.82	H-Bond (Ligand Donor)	false
CAI	CE	MET- 450	3.69	0	Hydrophobic	false
NAE	O	ALA- 451	2.81	124.8	H-Bond (Ligand Donor)	false
NAB	N	ALA- 451	2.95	160.33	H-Bond (Protein Donor)	false
OAS	O	GLU- 452	3.32	151.83	H-Bond (Ligand Donor)	false
CAL	CG	PRO- 455	4.34	0	Hydrophobic	false
SAO	CD1	LEU- 501	4.02	0	Hydrophobic	false