scPDB - 3v9y entry

Protein Data Bank Entry:

PDB ID : 3v9y

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2011-12-28

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:	27.703
Number of residues:	40
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.387	911.250

% Hydrophobic	% Polar
59.63	40.37
According to VolSite

Ligand :

HET Code:	24L
Formula:	C32H27NO9
Molecular weight:	569.558 g/mol
DrugBank ID:	-
Buried Surface Area:	69.36 %
Polar Surface area:	165.12 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	2
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
12.0126	49.0653	59.9853

Binding mode :

What is Poseview ?

2D View
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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
C17	CB	ILE- 262	3.84	0	Hydrophobic	false
C1	CG	LYS- 263	3.48	0	Hydrophobic	false
O18	NH1	ARG- 280	2.74	143.22	H-Bond (Protein Donor)	false
O18	NH2	ARG- 280	2.77	141.27	H-Bond (Protein Donor)	false
C14	CG2	ILE- 281	3.87	0	Hydrophobic	false
C22	CG2	ILE- 281	4.17	0	Hydrophobic	false
C22	SG	CYS- 285	3.89	0	Hydrophobic	false
C15	SG	CYS- 285	3.66	0	Hydrophobic	false
C29	SG	CYS- 285	4.12	0	Hydrophobic	false
C32	CB	CYS- 285	3.7	0	Hydrophobic	false
C27	SG	CYS- 285	3.77	0	Hydrophobic	false
C38	CB	CYS- 285	3.96	0	Hydrophobic	false
C39	CG	GLN- 286	4.27	0	Hydrophobic	false
C11	CB	ARG- 288	4.45	0	Hydrophobic	false
C39	CB	SER- 289	4.29	0	Hydrophobic	false
O41	OG	SER- 289	2.7	154.68	H-Bond (Protein Donor)	false
O41	NE2	HIS- 323	2.95	134.75	H-Bond (Protein Donor)	false
C27	CD1	LEU- 330	3.94	0	Hydrophobic	false
C29	CD1	LEU- 330	3.76	0	Hydrophobic	false
C28	CD1	LEU- 330	3.59	0	Hydrophobic	false
C35	CE	MET- 334	3.59	0	Hydrophobic	false
C22	CG1	VAL- 339	4.11	0	Hydrophobic	false
C35	CG1	VAL- 339	4.14	0	Hydrophobic	false
C17	CD1	ILE- 341	4	0	Hydrophobic	false
C13	CD1	ILE- 341	3.95	0	Hydrophobic	false
C16	CG2	ILE- 341	3.67	0	Hydrophobic	false
C22	SD	MET- 348	3.78	0	Hydrophobic	false
C14	CE	MET- 348	3.68	0	Hydrophobic	false
C22	CD1	LEU- 353	3.43	0	Hydrophobic	false
C35	CD1	LEU- 353	4.5	0	Hydrophobic	false
C37	CZ	PHE- 363	4.23	0	Hydrophobic	false
C38	CE2	PHE- 363	3.38	0	Hydrophobic	false
C39	CZ	PHE- 363	3.91	0	Hydrophobic	false
C33	SD	MET- 364	3.77	0	Hydrophobic	false
C34	CB	LYS- 367	3.83	0	Hydrophobic	false
C33	CG	LYS- 367	3.4	0	Hydrophobic	false
O42	NE2	HIS- 449	3.07	139.04	H-Bond (Protein Donor)	false
C39	CD1	LEU- 469	4.34	0	Hydrophobic	false
O42	OH	TYR- 473	2.69	146.29	H-Bond (Protein Donor)	false