scPDB - 4dgg entry

Protein Data Bank Entry:

PDB ID : 4dgg

Resolution :2.650 Å

Experimental Method : X-ray

Deposition Date : 2012-01-25

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
A	100 %

Ligand binding site composition:

B-Factor:	44.570
Number of residues:	38
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.617	961.875

% Hydrophobic	% Polar
61.05	38.95
According to VolSite

Ligand :

HET Code:	I76
Formula:	C25H22ClN5O
Molecular weight:	443.928 g/mol
DrugBank ID:	-
Buried Surface Area:	56.08 %
Polar Surface area:	78.85 Å2

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

Mass center Coordinates

X	Y	Z
-4.84697	-36.1361	8.79066

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
CAA	CB	LEU- 273	3.89	0	Hydrophobic	false
C5	CG1	VAL- 281	4.28	0	Hydrophobic	false
CAA	CG1	VAL- 281	3.66	0	Hydrophobic	false
CAO	CG1	VAL- 281	4.4	0	Hydrophobic	false
C5	CB	ALA- 293	4.08	0	Hydrophobic	false
CAP	CD	LYS- 295	4.25	0	Hydrophobic	false
CAJ	CB	LYS- 295	3.68	0	Hydrophobic	false
CBA	CD	LYS- 295	3.99	0	Hydrophobic	false
CLD	CE1	PHE- 307	4.43	0	Hydrophobic	false
CLD	CB	ALA- 311	3.73	0	Hydrophobic	false
CAW	CE	MET- 314	4.19	0	Hydrophobic	false
CAM	SD	MET- 314	4	0	Hydrophobic	false
CLD	CB	MET- 314	4.32	0	Hydrophobic	false
CLD	CD1	LEU- 325	4.42	0	Hydrophobic	false
CAH	CG2	ILE- 336	3.98	0	Hydrophobic	false
CAV	CD1	ILE- 336	4.39	0	Hydrophobic	false
CLD	CG2	ILE- 336	4.31	0	Hydrophobic	false
CAM	CG1	ILE- 336	4.04	0	Hydrophobic	false
CAJ	CG2	THR- 338	3.54	0	Hydrophobic	false
NAC	O	GLU- 339	3.07	168.84	H-Bond (Ligand Donor)	false
N1	N	MET- 341	3.07	161.1	H-Bond (Protein Donor)	false
CAB	CD2	LEU- 393	4.06	0	Hydrophobic	false
C5	CD1	LEU- 393	3.44	0	Hydrophobic	false
CAY	CD1	LEU- 393	4.07	0	Hydrophobic	false
CAK	CB	ASP- 404	4.21	0	Hydrophobic	false