scPDB - 2om9 entry

Protein Data Bank Entry:

PDB ID : 2om9

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2007-01-21

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
D	100 %

Ligand binding site composition:

B-Factor:	47.887
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.381	1414.125

% Hydrophobic	% Polar
60.38	39.62
According to VolSite

Ligand :

HET Code:	AJA
Formula:	C25H35O4
Molecular weight:	399.543 g/mol
DrugBank ID:	DB12193
Buried Surface Area:	61.42 %
Polar Surface area:	69.59 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	3
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
19.9042	21.7422	-79.2828

Binding mode :

What is Poseview ?

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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
C18	CD1	LEU- 255	3.8	0	Hydrophobic	false
C12	CE2	PHE- 264	3.34	0	Hydrophobic	false
C21	CG2	ILE- 281	4.37	0	Hydrophobic	false
C29	CG2	ILE- 281	4.14	0	Hydrophobic	false
C28	CD2	PHE- 282	4.05	0	Hydrophobic	false
C29	CB	PHE- 282	4.36	0	Hydrophobic	false
C22	SG	CYS- 285	3.6	0	Hydrophobic	false
C21	CB	CYS- 285	4.22	0	Hydrophobic	false
C6	CB	CYS- 285	3.91	0	Hydrophobic	false
C25	CD1	LEU- 330	4.23	0	Hydrophobic	false
C25	CG1	VAL- 339	4.12	0	Hydrophobic	false
C24	CG1	VAL- 339	3.76	0	Hydrophobic	false
C9	CB	ILE- 341	4.34	0	Hydrophobic	false
C13	CD1	ILE- 341	4.39	0	Hydrophobic	false
C5	CG2	ILE- 341	3.48	0	Hydrophobic	false
O27	OG	SER- 342	3.19	165.9	H-Bond (Protein Donor)	false
C24	SD	MET- 348	3.97	0	Hydrophobic	false
C3	SD	MET- 348	4.15	0	Hydrophobic	false
C2	CE	MET- 348	4.24	0	Hydrophobic	false
C18	CE	MET- 348	4.03	0	Hydrophobic	false
C21	CD2	LEU- 353	4	0	Hydrophobic	false
C23	CD2	LEU- 353	4.34	0	Hydrophobic	false
C24	CD1	LEU- 353	3.8	0	Hydrophobic	false
C29	CD1	LEU- 356	3.87	0	Hydrophobic	false
C29	CB	PHE- 360	4.08	0	Hydrophobic	false
C25	CE	MET- 364	4.34	0	Hydrophobic	false
C20	SD	MET- 364	3.82	0	Hydrophobic	false
C21	CG	MET- 364	4.23	0	Hydrophobic	false
C22	SD	MET- 364	4.38	0	Hydrophobic	false
C23	CG	MET- 364	3.9	0	Hydrophobic	false