scPDB - 4y93 entry

Protein Data Bank Entry:

PDB ID : 4y93

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2015-02-16

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
ID:	Q3ZC95_BOVIN
AC:	Q3ZC95
Organism:	Bos taurus
Reign:	Eukaryota
TaxID:	9913
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	14.840
Number of residues:	43
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
1.343	793.125

% Hydrophobic	% Polar
50.64	49.36
According to VolSite

Ligand :

HET Code:	746
Formula:	C34H37N5O4
Molecular weight:	579.689 g/mol
DrugBank ID:	-
Buried Surface Area:	55.91 %
Polar Surface area:	103.33 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
29.9627	-47.6425	344.949

Binding mode :

What is Poseview ?

2D View
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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
C9	CB	LEU- 408	4.2	0	Hydrophobic	false
C48	CB	LEU- 408	3.9	0	Hydrophobic	false
C51	CD2	LEU- 408	3.95	0	Hydrophobic	false
C26	CB	GLN- 412	3.66	0	Hydrophobic	false
C34	CB	GLN- 412	4.05	0	Hydrophobic	false
C38	CE2	PHE- 413	4.09	0	Hydrophobic	false
C9	CB	VAL- 416	3.75	0	Hydrophobic	false
C1	CG2	VAL- 416	4.02	0	Hydrophobic	false
C7	CG2	VAL- 416	3.72	0	Hydrophobic	false
C60	CB	ALA- 428	3.39	0	Hydrophobic	false
O15	N	MET- 477	2.73	162.12	H-Bond (Protein Donor)	false
N47	O	MET- 477	2.96	141.65	H-Bond (Ligand Donor)	false
C42	CB	ASP- 521	4.18	0	Hydrophobic	false
C3	CD1	LEU- 528	4.44	0	Hydrophobic	false
C60	CD1	LEU- 528	3.56	0	Hydrophobic	false
C42	CB	ASP- 539	4.12	0	Hydrophobic	false
C29	CB	ASP- 539	4.17	0	Hydrophobic	false
C38	CB	MET- 542	4.05	0	Hydrophobic	false
C38	CG2	THR- 543	4.35	0	Hydrophobic	false
C42	CG2	THR- 543	4.08	0	Hydrophobic	false
C38	CG2	VAL- 546	3.69	0	Hydrophobic	false
C34	CZ	TYR- 551	3.75	0	Hydrophobic	false
O22	O	HOH- 964	2.89	179.97	H-Bond (Protein Donor)	false