scPDB - 1yol entry

Protein Data Bank Entry:

PDB ID : 1yol

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2005-01-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Proto-oncogene tyrosine-protein kinase Src
ID:	SRC_HUMAN
AC:	P12931
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.10.2

Chains:

Chain Name:	Percentage of Residues within binding site
A	86 %
B	14 %

Ligand binding site composition:

B-Factor:	49.768
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.034	577.125

% Hydrophobic	% Polar
52.63	47.37
According to VolSite

Ligand :

HET Code:	S03
Formula:	C25H28N5O2
Molecular weight:	430.522 g/mol
DrugBank ID:	-
Buried Surface Area:	57.57 %
Polar Surface area:	90.63 Å2

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

Mass center Coordinates

X	Y	Z
2.89403	23.3828	29.2883

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
C2	CG1	VAL- 283	4.16	0	Hydrophobic	false
C19	CB	VAL- 283	4.48	0	Hydrophobic	false
C15	CG1	VAL- 283	4.1	0	Hydrophobic	false
C2	CB	ALA- 295	4.27	0	Hydrophobic	false
C15	CB	ALA- 295	4.04	0	Hydrophobic	false
C17	CB	LYS- 297	3.4	0	Hydrophobic	false
C13	CD	LYS- 297	3.92	0	Hydrophobic	false
C14	CG	LYS- 297	3.97	0	Hydrophobic	false
C17	CG2	ILE- 338	3.56	0	Hydrophobic	false
C17	CG2	THR- 340	3.35	0	Hydrophobic	false
C14	CG2	THR- 340	3.71	0	Hydrophobic	false
N33	O	GLU- 341	3.21	165.46	H-Bond (Ligand Donor)	false
N6	N	MET- 343	3.09	164.53	H-Bond (Protein Donor)	false
C22	CB	SER- 347	3.8	0	Hydrophobic	false
N26	OD2	ASP- 350	3.36	0	Ionic (Ligand Cationic)	false
C2	CD1	LEU- 395	3.39	0	Hydrophobic	false
C10	CD1	LEU- 395	3.98	0	Hydrophobic	false
C23	CD2	LEU- 395	3.87	0	Hydrophobic	false
C11	CB	ALA- 405	4.22	0	Hydrophobic	false
O32	O	THR- 525	3.28	133.31	H-Bond (Ligand Donor)	false