scPDB - 2f3m entry

Protein Data Bank Entry:

PDB ID : 2f3m

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2005-11-21

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 Mu 1
ID:	GSTM1_HUMAN
AC:	P09488
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.5.1.18

Chains:

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

Ligand binding site composition:

B-Factor:	51.075
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.453	587.250

% Hydrophobic	% Polar
39.66	60.34
According to VolSite

Ligand :

HET Code:	GTD
Formula:	C16H19N6O12S
Molecular weight:	519.420 g/mol
DrugBank ID:	-
Buried Surface Area:	56.88 %
Polar Surface area:	328.85 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	3
Rings:	1
Aromatic rings:	0
Anionic atoms:	5
Cationic atoms:	4
Rule of Five Violation:	2
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
-59.7932	-86.6839	51.4837

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
O2	NE1	TRP- 7	2.95	170.67	H-Bond (Protein Donor)	false
SG2	CD1	LEU- 12	3.41	0	Hydrophobic	false
CB1	CD1	LEU- 12	3.93	0	Hydrophobic	false
O32	NE1	TRP- 45	3.13	168.71	H-Bond (Protein Donor)	false
O31	NZ	LYS- 49	3.85	0	Ionic (Protein Cationic)	false
O32	NZ	LYS- 49	2.55	0	Ionic (Protein Cationic)	false
O32	NZ	LYS- 49	2.55	170.78	H-Bond (Protein Donor)	false
N3	OD1	ASN- 58	3.14	126.22	H-Bond (Ligand Donor)	false
N2	O	LEU- 59	2.9	166.37	H-Bond (Ligand Donor)	false
N1	OE1	GLN- 71	2.88	142.75	H-Bond (Ligand Donor)	false
O11	N	SER- 72	2.57	173.16	H-Bond (Protein Donor)	false
O12	OG	SER- 72	3.25	150.65	H-Bond (Protein Donor)	false
N1	OD1	ASP- 105	3.61	0	Ionic (Ligand Cationic)	false
N1	OD2	ASP- 105	2.8	0	Ionic (Ligand Cationic)	false
N1	OD2	ASP- 105	2.8	148.7	H-Bond (Ligand Donor)	false
O22	NE2	HIS- 107	3.43	158.83	H-Bond (Protein Donor)	false
C1'	CZ	TYR- 115	4.44	0	Hydrophobic	false
N2'	OH	TYR- 115	3.28	150.84	H-Bond (Protein Donor)	false
O21	OH	TYR- 115	2.75	147.13	H-Bond (Protein Donor)	false
O11	O	HOH- 5221	2.81	179.98	H-Bond (Protein Donor)	false