scPDB - 5agy entry

Protein Data Bank Entry:

PDB ID : 5agy

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2015-02-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tau class glutathione S-transferase
ID:	I1MJ34_SOYBN
AC:	I1MJ34
Organism:	Glycine max
Reign:	Eukaryota
TaxID:	3847
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	7 %
B	93 %

Ligand binding site composition:

B-Factor:	23.704
Number of residues:	32
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.660	421.875

% Hydrophobic	% Polar
64.80	35.20
According to VolSite

Ligand :

HET Code:	GTB
Formula:	C17H21N4O8S
Molecular weight:	441.436 g/mol
DrugBank ID:	DB03686
Buried Surface Area:	52.81 %
Polar Surface area:	237.22 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	1
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
35.8574	-8.39237	-8.77887

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
SG2	CB	SER- 13	3.55	0	Hydrophobic	false
SG2	CD2	PHE- 15	3.84	0	Hydrophobic	false
C'	CE2	PHE- 15	4.16	0	Hydrophobic	false
CG1	CD2	PHE- 15	3.6	0	Hydrophobic	false
CB2	CD1	LEU- 37	3.71	0	Hydrophobic	false
O32	NZ	LYS- 40	2.64	175.07	H-Bond (Protein Donor)	false
O32	NZ	LYS- 40	2.64	0	Ionic (Protein Cationic)	false
CG1	CD	LYS- 53	4.17	0	Hydrophobic	false
N2	O	ILE- 54	2.76	156.58	H-Bond (Ligand Donor)	false
O2	N	ILE- 54	2.93	152.35	H-Bond (Protein Donor)	false
CB2	CD1	ILE- 54	3.75	0	Hydrophobic	false
N1	OE1	GLU- 66	2.72	152.45	H-Bond (Ligand Donor)	false
O11	N	SER- 67	3.39	145.01	H-Bond (Protein Donor)	false
O11	OG	SER- 67	2.7	158.05	H-Bond (Protein Donor)	false
O12	N	SER- 67	2.84	156.38	H-Bond (Protein Donor)	false
C'	CZ	TYR- 107	3.56	0	Hydrophobic	false
O11	O	HOH- 2018	2.81	179.99	H-Bond (Protein Donor)	false
O12	O	HOH- 2081	2.87	179.96	H-Bond (Protein Donor)	false
N1	O	HOH- 2143	2.83	155.86	H-Bond (Ligand Donor)	false