scPDB - 4fyo entry

Protein Data Bank Entry:

PDB ID : 4fyo

Resolution :1.400 Å

Experimental Method : X-ray

Deposition Date : 2012-07-05

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:	22.887
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.031	415.125

% Hydrophobic	% Polar
61.79	38.21
According to VolSite

Ligand :

HET Code:	0VF
Formula:	C25H23N6O5S
Molecular weight:	519.552 g/mol
DrugBank ID:	-
Buried Surface Area:	55.08 %
Polar Surface area:	169.86 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	2
Rings:	5
Aromatic rings:	4
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-0.586459	2.02751	13.5334

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
C19	CD1	LEU- 377	4.19	0	Hydrophobic	false
C36	CB	LEU- 377	4.24	0	Hydrophobic	false
C31	CD2	LEU- 377	4.1	0	Hydrophobic	false
C21	CG2	VAL- 385	3.67	0	Hydrophobic	false
S9	CB	ALA- 400	3.83	0	Hydrophobic	false
S9	CG1	VAL- 433	3.96	0	Hydrophobic	false
S9	SD	MET- 448	3.95	0	Hydrophobic	false
C33	SD	MET- 450	4.16	0	Hydrophobic	false
N8	N	ALA- 451	3.19	166.15	H-Bond (Protein Donor)	false
N11	O	ALA- 451	3.29	129.08	H-Bond (Ligand Donor)	false
C36	CG	PRO- 455	4.33	0	Hydrophobic	false
C27	CG	PRO- 455	3.79	0	Hydrophobic	false
O32	ND2	ASN- 457	2.7	148.41	H-Bond (Protein Donor)	false
O32	NZ	LYS- 458	3.55	0	Ionic (Protein Cationic)	false
C30	CG	LYS- 458	4.14	0	Hydrophobic	false
C29	CD	ARG- 498	4.03	0	Hydrophobic	false
C20	CB	ARG- 498	3.77	0	Hydrophobic	false
S9	CD1	LEU- 501	3.5	0	Hydrophobic	false