scPDB - 3tub entry

Protein Data Bank Entry:

PDB ID : 3tub

Resolution :2.230 Å

Experimental Method : X-ray

Deposition Date : 2011-09-16

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:	48.355
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.523	651.375

% Hydrophobic	% Polar
70.98	29.02
According to VolSite

Ligand :

HET Code:	FPU
Formula:	C26H24N4O4
Molecular weight:	456.493 g/mol
DrugBank ID:	-
Buried Surface Area:	69.12 %
Polar Surface area:	94.6 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
22.2318	-4.52679	-9.57388

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
C1	CB	LEU- 377	3.98	0	Hydrophobic	false
C2	CB	LEU- 377	4.24	0	Hydrophobic	false
C11	CD2	LEU- 377	3.63	0	Hydrophobic	false
C10	CD1	LEU- 377	4.13	0	Hydrophobic	false
C13	CG2	VAL- 385	3.89	0	Hydrophobic	false
C5	CG1	VAL- 385	3.96	0	Hydrophobic	false
C6	CB	ALA- 400	3.65	0	Hydrophobic	false
C14	CD	LYS- 402	3.82	0	Hydrophobic	false
N3	OE2	GLU- 420	2.9	156.7	H-Bond (Ligand Donor)	false
N4	OE2	GLU- 420	3.03	141.08	H-Bond (Ligand Donor)	false
C19	CG	GLU- 420	4.13	0	Hydrophobic	false
C19	CG1	VAL- 423	4.04	0	Hydrophobic	false
C20	CG	MET- 424	3.74	0	Hydrophobic	false
C23	CD2	LEU- 427	3.69	0	Hydrophobic	false
C26	CG2	ILE- 432	4.41	0	Hydrophobic	false
C25	CG1	ILE- 432	3.68	0	Hydrophobic	false
C6	CG1	VAL- 433	4.25	0	Hydrophobic	false
C6	CG	MET- 448	3.82	0	Hydrophobic	false
C13	SD	MET- 448	3.84	0	Hydrophobic	false
C9	SD	MET- 450	3.78	0	Hydrophobic	false
N1	N	ALA- 451	3	156.85	H-Bond (Protein Donor)	false
C9	CB	ALA- 451	4.28	0	Hydrophobic	false
C24	CD1	LEU- 485	3.77	0	Hydrophobic	false
C5	CD1	LEU- 501	3.87	0	Hydrophobic	false
C24	CG2	ILE- 510	3.97	0	Hydrophobic	false
O4	N	ASP- 512	2.71	173.4	H-Bond (Protein Donor)	false
C22	CB	ASP- 512	3.4	0	Hydrophobic	false
C19	CD1	LEU- 515	3.83	0	Hydrophobic	false