scPDB - 3pgt entry

Protein Data Bank Entry:

PDB ID : 3pgt

Resolution :2.140 Å

Experimental Method : X-ray

Deposition Date : 1999-03-22

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 P
ID:	GSTP1_HUMAN
AC:	P09211
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.5.1.18

Chains:

Chain Name:	Percentage of Residues within binding site
A	89 %
B	11 %

Ligand binding site composition:

B-Factor:	13.610
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.823	830.250

% Hydrophobic	% Polar
41.87	58.13
According to VolSite

Ligand :

HET Code:	GBX
Formula:	C30H26N3O9S
Molecular weight:	604.607 g/mol
DrugBank ID:	-
Buried Surface Area:	45.62 %
Polar Surface area:	245.77 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	5
Aromatic rings:	4
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
26.2402	-6.75158	6.77693

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
SG2	CE2	PHE- 8	3.74	0	Hydrophobic	false
C5'	CB	PHE- 8	3.69	0	Hydrophobic	false
C6'	CG1	VAL- 10	3.65	0	Hydrophobic	false
O12	CZ	ARG- 13	3.51	0	Ionic (Protein Cationic)	false
CG1	CD	ARG- 13	4.21	0	Hydrophobic	false
O31	NE1	TRP- 38	2.91	162.78	H-Bond (Protein Donor)	false
O31	NZ	LYS- 44	2.83	165.43	H-Bond (Protein Donor)	false
O31	NZ	LYS- 44	2.83	0	Ionic (Protein Cationic)	false
O32	NZ	LYS- 44	3.54	0	Ionic (Protein Cationic)	false
CG1	CB	GLN- 51	4.16	0	Hydrophobic	false
O32	NE2	GLN- 51	3.22	170.7	H-Bond (Protein Donor)	false
O2	N	LEU- 52	2.76	167.71	H-Bond (Protein Donor)	false
N2	O	LEU- 52	2.77	140.22	H-Bond (Ligand Donor)	false
O11	N	SER- 65	2.83	156.6	H-Bond (Protein Donor)	false
O12	N	SER- 65	3.47	147.17	H-Bond (Protein Donor)	false
O12	OG	SER- 65	2.94	167.19	H-Bond (Protein Donor)	false
N1	OD2	ASP- 98	2.61	131.31	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 98	2.61	0	Ionic (Ligand Cationic)	false
N1	OD1	ASP- 98	3.33	0	Ionic (Ligand Cationic)	false
C7	CD1	TYR- 108	3.96	0	Hydrophobic	false
C9	CE2	TYR- 108	4.37	0	Hydrophobic	false
C10	CZ	TYR- 108	4.37	0	Hydrophobic	false
C1'	CE1	TYR- 108	3.3	0	Hydrophobic	false
C9A	CB	ASN- 206	4.36	0	Hydrophobic	false
O11	O	HOH- 301	3.08	152.78	H-Bond (Protein Donor)	false