scPDB - 1vf3 entry

Protein Data Bank Entry:

PDB ID : 1vf3

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2004-04-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutathione S-transferase 3
ID:	GSTA3_CHICK
AC:	P26697
Organism:	Gallus gallus
Reign:	Eukaryota
TaxID:	9031
EC Number:	2.5.1.18

Chains:

Chain Name:	Percentage of Residues within binding site
A	15 %
B	85 %

Ligand binding site composition:

B-Factor:	39.783
Number of residues:	37
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.893	1063.125

% Hydrophobic	% Polar
46.35	53.65
According to VolSite

Ligand :

HET Code:	GDN
Formula:	C16H18N5O10S
Molecular weight:	472.407 g/mol
DrugBank ID:	DB02458
Buried Surface Area:	67.05 %
Polar Surface area:	283.03 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	3
Rings:	1
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	3
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
14.567	23.5101	20.5231

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
N1	OD1	ASP- 101	3.64	0	Ionic (Ligand Cationic)	false
N1	OD2	ASP- 101	2.75	0	Ionic (Ligand Cationic)	false
N1	OD2	ASP- 101	2.75	168.38	H-Bond (Ligand Donor)	false
O31	NH1	ARG- 131	3.33	163.67	H-Bond (Protein Donor)	false
O32	NH2	ARG- 131	2.77	164.13	H-Bond (Protein Donor)	false
O32	CZ	ARG- 131	3.66	0	Ionic (Protein Cationic)	false
SG2	CE1	TYR- 1009	3.96	0	Hydrophobic	false
CB2	CE2	PHE- 1010	4.47	0	Hydrophobic	false
O12	NZ	LYS- 1015	2.95	150.37	H-Bond (Protein Donor)	false
O2A	N	LYS- 1015	3.03	125.51	H-Bond (Protein Donor)	false
O12	NZ	LYS- 1015	2.95	0	Ionic (Protein Cationic)	false
CG1	CD	LYS- 1015	4.44	0	Hydrophobic	false
CG1	CB	GLN- 1054	4.12	0	Hydrophobic	false
O31	NE2	GLN- 1054	3.39	172.06	H-Bond (Protein Donor)	false
N2	O	VAL- 1055	2.78	152.34	H-Bond (Ligand Donor)	false
O2	N	VAL- 1055	3.27	162	H-Bond (Protein Donor)	false
CB2	CG2	VAL- 1055	4.31	0	Hydrophobic	false
N1	OE1	GLN- 1067	2.86	137.29	H-Bond (Ligand Donor)	false
O11	N	THR- 1068	2.94	163.74	H-Bond (Protein Donor)	false
O11	OG1	THR- 1068	3.09	141.19	H-Bond (Protein Donor)	false
O12	OG1	THR- 1068	3.37	152.69	H-Bond (Protein Donor)	false
CB2	CD1	LEU- 1220	4.08	0	Hydrophobic	false
N3	OH	TYR- 1223	2.65	160.46	H-Bond (Ligand Donor)	false
O11	O	HOH- 4042	2.93	139.01	H-Bond (Protein Donor)	false