scPDB - 3vjh entry

Protein Data Bank Entry:

PDB ID : 3vjh

Resolution :2.220 Å

Experimental Method : X-ray

Deposition Date : 2011-10-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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:	63.760
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.624	1130.625

% Hydrophobic	% Polar
61.49	38.51
According to VolSite

Ligand :

HET Code:	J35
Formula:	C22H23F3NO4
Molecular weight:	422.418 g/mol
DrugBank ID:	-
Buried Surface Area:	59.31 %
Polar Surface area:	78.46 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
-17.2989	19.6445	-13.5873

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
C22	CE1	PHE- 282	3.29	0	Hydrophobic	false
C12	CB	CYS- 285	4.2	0	Hydrophobic	false
C10	SG	CYS- 285	4.09	0	Hydrophobic	false
C18	CB	CYS- 285	4.01	0	Hydrophobic	false
C2	SG	CYS- 285	3.27	0	Hydrophobic	false
C22	CG	GLN- 286	3.3	0	Hydrophobic	false
C8	CG	ARG- 288	3.75	0	Hydrophobic	false
C3	CB	ARG- 288	4.1	0	Hydrophobic	false
O3	OG	SER- 289	2.67	170.29	H-Bond (Protein Donor)	false
C20	CB	SER- 289	3.81	0	Hydrophobic	false
C14	CB	SER- 289	3.49	0	Hydrophobic	false
O3	NE2	HIS- 323	2.89	150.49	H-Bond (Protein Donor)	false
C14	CG2	ILE- 326	3.64	0	Hydrophobic	false
C17	CE1	TYR- 327	4.01	0	Hydrophobic	false
C11	CD1	LEU- 330	4.49	0	Hydrophobic	false
C8	CD1	LEU- 330	3.57	0	Hydrophobic	false
C10	CD2	LEU- 330	4.16	0	Hydrophobic	false
F1	CD1	ILE- 341	4.26	0	Hydrophobic	false
F3	CD1	ILE- 341	4.26	0	Hydrophobic	false
C2	CG2	ILE- 341	3.66	0	Hydrophobic	false
C12	CE	MET- 364	4.41	0	Hydrophobic	false
C22	CD1	LEU- 453	4.33	0	Hydrophobic	false
O2	OH	TYR- 473	2.64	147.73	H-Bond (Protein Donor)	false