scPDB - 4agw entry

Protein Data Bank Entry:

PDB ID : 4agw

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2012-02-01

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_CHICK
AC:	P00523
Organism:	Gallus gallus
Reign:	Eukaryota
TaxID:	9031
EC Number:	2.7.10.2

Chains:

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

Ligand binding site composition:

B-Factor:	53.262
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.596	1015.875

% Hydrophobic	% Polar
62.79	37.21
According to VolSite

Ligand :

HET Code:	NG7
Formula:	C31H32F3N6O2S
Molecular weight:	609.685 g/mol
DrugBank ID:	-
Buried Surface Area:	59.8 %
Polar Surface area:	119.9 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	6
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
9.85051	37.1945	-36.323

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
S	CD1	LEU- 273	3.8	0	Hydrophobic	false
C10	CD2	LEU- 273	4.17	0	Hydrophobic	false
C01	CB	ALA- 293	3.33	0	Hydrophobic	false
C12	CB	ALA- 293	4.01	0	Hydrophobic	false
C12	CB	LYS- 295	4.42	0	Hydrophobic	false
C13	CD	LYS- 295	3.65	0	Hydrophobic	false
N04	OE2	GLU- 310	2.65	160.86	H-Bond (Ligand Donor)	false
C19	CG	GLU- 310	3.24	0	Hydrophobic	false
C20	CG1	VAL- 313	4.17	0	Hydrophobic	false
C15	SD	MET- 314	4.24	0	Hydrophobic	false
C19	CG	MET- 314	3.91	0	Hydrophobic	false
C23	CG	MET- 314	4	0	Hydrophobic	false
F3	CD1	LEU- 317	3.5	0	Hydrophobic	false
F3	CD2	LEU- 322	3.58	0	Hydrophobic	false
F2	CG	LEU- 322	3.82	0	Hydrophobic	false
C05	CG1	VAL- 323	4.12	0	Hydrophobic	false
C16	CG1	VAL- 323	3.81	0	Hydrophobic	false
C05	CB	THR- 338	4.29	0	Hydrophobic	false
C13	CG2	THR- 338	4.19	0	Hydrophobic	false
S	CE1	TYR- 340	4.34	0	Hydrophobic	false
C08	CZ	TYR- 340	4.18	0	Hydrophobic	false
C01	CG	MET- 341	4.03	0	Hydrophobic	false
N02	N	MET- 341	2.98	158.58	H-Bond (Protein Donor)	false
N03	O	MET- 341	2.75	139.06	H-Bond (Ligand Donor)	false
N	O	VAL- 383	2.75	150.27	H-Bond (Ligand Donor)	false
C30	CD	ARG- 385	3.34	0	Hydrophobic	false
S	CD2	LEU- 393	4.39	0	Hydrophobic	false
C01	CD1	LEU- 393	3.48	0	Hydrophobic	false
F1	CG1	VAL- 402	3.36	0	Hydrophobic	false
O	N	ASP- 404	2.74	160.11	H-Bond (Protein Donor)	false
C23	CB	ASP- 404	3.51	0	Hydrophobic	false