scPDB - 3rpn entry

Protein Data Bank Entry:

PDB ID : 3rpn

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2011-04-27

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 kappa 1
ID:	GSTK1_HUMAN
AC:	Q9Y2Q3
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.5.1.18

Chains:

Chain Name:	Percentage of Residues within binding site
C	11 %
F	89 %

Ligand binding site composition:

B-Factor:	38.294
Number of residues:	39
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.901	1653.750

% Hydrophobic	% Polar
66.53	33.47
According to VolSite

Ligand :

HET Code:	GTX
Formula:	C16H28N3O6S
Molecular weight:	390.475 g/mol
DrugBank ID:	-
Buried Surface Area:	62.38 %
Polar Surface area:	191.4 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	0
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
-1.90069	-70.1389	35.4587

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	CB	SER- 16	3.75	0	Hydrophobic	false
C4S	CG	PRO- 17	3.43	0	Hydrophobic	false
C2S	CD2	TYR- 18	3.95	0	Hydrophobic	false
CG1	CG	TYR- 18	3.76	0	Hydrophobic	false
SG2	CD2	TYR- 18	3.64	0	Hydrophobic	false
O31	ND2	ASN- 53	2.84	161.08	H-Bond (Protein Donor)	false
O31	NZ	LYS- 62	2.5	158.55	H-Bond (Protein Donor)	false
O31	NZ	LYS- 62	2.5	0	Ionic (Protein Cationic)	false
O32	NZ	LYS- 62	3.84	0	Ionic (Protein Cationic)	false
C1S	CE	MET- 66	3.73	0	Hydrophobic	false
C5S	CE	MET- 66	3.22	0	Hydrophobic	false
C6S	CD1	LEU- 70	3.92	0	Hydrophobic	false
C5S	CD1	LEU- 88	3.65	0	Hydrophobic	false
C6S	CH2	TRP- 126	3.59	0	Hydrophobic	false
N2	O	LEU- 183	2.75	142.24	H-Bond (Ligand Donor)	false
O2	N	LEU- 183	2.96	140.05	H-Bond (Protein Donor)	false
CG1	CZ	PHE- 198	3.69	0	Hydrophobic	false
O11	OG	SER- 200	3	170.23	H-Bond (Protein Donor)	false
O11	N	SER- 200	2.62	171.15	H-Bond (Protein Donor)	false
O12	OG	SER- 200	2.93	127.2	H-Bond (Protein Donor)	false
N1	OD1	ASP- 201	3.92	0	Ionic (Ligand Cationic)	false
N1	OD2	ASP- 201	2.8	0	Ionic (Ligand Cationic)	false
N1	OD2	ASP- 201	2.8	141.58	H-Bond (Ligand Donor)	false
O12	NH2	ARG- 202	3.2	163.04	H-Bond (Protein Donor)	false