scPDB - 4dfn entry

Protein Data Bank Entry:

PDB ID : 4dfn

Resolution :2.480 Å

Experimental Method : X-ray

Deposition Date : 2012-01-24

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:	68.746
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.053	793.125

% Hydrophobic	% Polar
51.49	48.51
According to VolSite

Ligand :

HET Code:	0K1
Formula:	C25H28N6O2
Molecular weight:	444.529 g/mol
DrugBank ID:	-
Buried Surface Area:	66.27 %
Polar Surface area:	118.95 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	7
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
1.52636	1.76688	13.1093

Binding mode :

What is Poseview ?

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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
C3	CD1	LEU- 377	3.7	0	Hydrophobic	false
C6	CB	LEU- 377	3.79	0	Hydrophobic	false
C32	CE2	PHE- 382	4.3	0	Hydrophobic	false
C29	CE1	PHE- 382	3.83	0	Hydrophobic	false
C28	CZ	PHE- 382	3.76	0	Hydrophobic	false
C28	CG2	VAL- 385	3.53	0	Hydrophobic	false
C29	CD	LYS- 402	4.15	0	Hydrophobic	false
N13	O	GLU- 449	2.86	157.07	H-Bond (Ligand Donor)	false
C3	CE	MET- 450	4.11	0	Hydrophobic	false
N9	N	ALA- 451	2.89	168.78	H-Bond (Protein Donor)	false
C4	CG	PRO- 455	4.37	0	Hydrophobic	false
DuAr	NZ	LYS- 458	3.51	73.34	Pi/Cation	false
C25	CD2	LEU- 501	4.15	0	Hydrophobic	false
C24	CB	SER- 511	4.31	0	Hydrophobic	false
C26	CB	ASP- 512	3.51	0	Hydrophobic	false