scPDB - 3vsp entry

Protein Data Bank Entry:

PDB ID : 3vsp

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2012-04-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	8.550	8.550	8.550	0.000	8.550	1

List of CHEMBLId :

CHEMBL3317858

Binding Site :

Uniprot Annotation

Name:	Peroxisome proliferator-activated receptor gamma
ID:	PPARG_HUMAN
AC:	P37231
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	54.565
Number of residues:	41
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.603	1137.375

% Hydrophobic	% Polar
61.42	38.58
According to VolSite

Ligand :

HET Code:	EK8
Formula:	C32H37N2O4
Molecular weight:	513.647 g/mol
DrugBank ID:	-
Buried Surface Area:	68.55 %
Polar Surface area:	81.7 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
17.8222	70.0953	12.6698

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
C84	CD1	LEU- 255	4.37	0	Hydrophobic	false
C83	CE1	PHE- 264	3.56	0	Hydrophobic	false
C99	CG2	ILE- 281	4.31	0	Hydrophobic	false
C22	SG	CYS- 285	4.13	0	Hydrophobic	false
C9	SG	CYS- 285	3.87	0	Hydrophobic	false
C12	SG	CYS- 285	3.26	0	Hydrophobic	false
C3	CB	CYS- 285	3.76	0	Hydrophobic	false
C7	CB	CYS- 285	3.87	0	Hydrophobic	false
C52	CG	GLN- 286	3.52	0	Hydrophobic	false
C7	CG	ARG- 288	4.42	0	Hydrophobic	false
C4	CB	SER- 289	4.46	0	Hydrophobic	false
C5	CB	SER- 289	3.45	0	Hydrophobic	false
C3	CB	SER- 289	3.41	0	Hydrophobic	false
O2	OG	SER- 289	2.74	158.1	H-Bond (Protein Donor)	false
O2	NE2	HIS- 323	3.2	141.03	H-Bond (Protein Donor)	false
C5	CG2	ILE- 326	4.28	0	Hydrophobic	false
C8	CD1	LEU- 330	4.38	0	Hydrophobic	false
C10	CD2	LEU- 330	4.28	0	Hydrophobic	false
C14	CG1	VAL- 339	3.58	0	Hydrophobic	false
C99	CD1	ILE- 341	4.45	0	Hydrophobic	false
C22	CG2	ILE- 341	3.85	0	Hydrophobic	false
C14	CG2	ILE- 341	3.66	0	Hydrophobic	false
C87	CB	ILE- 341	3.95	0	Hydrophobic	false
C84	CE	MET- 348	4.33	0	Hydrophobic	false
C99	CE	MET- 348	4.41	0	Hydrophobic	false
C14	SD	MET- 348	3.42	0	Hydrophobic	false
C13	CD1	LEU- 353	3.47	0	Hydrophobic	false
C9	CE	MET- 364	4.07	0	Hydrophobic	false
C13	CE	MET- 364	3.81	0	Hydrophobic	false
C10	SD	MET- 364	3.22	0	Hydrophobic	false
C53	CD1	LEU- 453	3.49	0	Hydrophobic	false
C52	CD2	LEU- 465	4.5	0	Hydrophobic	false
C51	CD2	LEU- 469	3.35	0	Hydrophobic	false