scPDB - 2p4y entry

Protein Data Bank Entry:

PDB ID : 2p4y

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2007-03-13

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:	41.016
Number of residues:	40
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.437	864.000

% Hydrophobic	% Polar
62.11	37.89
According to VolSite

Ligand :

HET Code:	C03
Formula:	C28H21ClF3N2O6
Molecular weight:	573.924 g/mol
DrugBank ID:	-
Buried Surface Area:	66.87 %
Polar Surface area:	98.78 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	0
Rings:	5
Aromatic rings:	5
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
14.7588	5.65682	12.6282

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
C58	CE2	PHE- 226	3.53	0	Hydrophobic	false
C30	CG2	ILE- 281	3.89	0	Hydrophobic	false
C5	CB	CYS- 285	3.65	0	Hydrophobic	false
C24	SG	CYS- 285	3.76	0	Hydrophobic	false
C31	SG	CYS- 285	3.59	0	Hydrophobic	false
C31	SG	CYS- 285	3.59	0	Hydrophobic	false
C38	CD	ARG- 288	3.5	0	Hydrophobic	false
C3	CB	ARG- 288	3.81	0	Hydrophobic	false
C1	CB	SER- 289	4.01	0	Hydrophobic	false
C58	CB	ALA- 292	3.58	0	Hydrophobic	false
C51	CB	ALA- 292	3.75	0	Hydrophobic	false
C58	CG1	ILE- 296	3.51	0	Hydrophobic	false
F23	CG2	ILE- 326	3.89	0	Hydrophobic	false
C1	CG2	ILE- 326	3.99	0	Hydrophobic	false
C52	CG2	ILE- 326	4.08	0	Hydrophobic	false
F23	CE2	TYR- 327	3.31	0	Hydrophobic	false
C58	CG	MET- 329	4.21	0	Hydrophobic	false
C51	CB	MET- 329	3.6	0	Hydrophobic	false
C5	CD2	LEU- 330	4.47	0	Hydrophobic	false
C14	CD1	LEU- 330	4.42	0	Hydrophobic	false
C18	CD1	LEU- 330	4.38	0	Hydrophobic	false
F22	CD2	LEU- 330	3.68	0	Hydrophobic	false
C53	CD1	LEU- 330	4.34	0	Hydrophobic	false
C4	CD1	LEU- 330	3.86	0	Hydrophobic	false
C14	CD2	LEU- 333	3.86	0	Hydrophobic	false
C49	CD2	LEU- 333	4.03	0	Hydrophobic	false
C14	CG2	VAL- 339	4.49	0	Hydrophobic	false
C18	CG2	VAL- 339	4.29	0	Hydrophobic	false
CL1	CG1	VAL- 339	3.64	0	Hydrophobic	false
C24	CG2	ILE- 341	3.65	0	Hydrophobic	false
C31	CG2	ILE- 341	3.6	0	Hydrophobic	false
C31	CG2	ILE- 341	3.6	0	Hydrophobic	false
O45	N	SER- 342	2.57	153.59	H-Bond (Protein Donor)	false
C30	SD	MET- 348	4.11	0	Hydrophobic	false
CL1	SD	MET- 348	4.2	0	Hydrophobic	false
CL1	CD1	LEU- 353	3.66	0	Hydrophobic	false
F21	CE1	PHE- 363	3.42	0	Hydrophobic	false
C20	CZ	PHE- 363	4.28	0	Hydrophobic	false
C5	CE	MET- 364	4.18	0	Hydrophobic	false
C18	CE	MET- 364	3.74	0	Hydrophobic	false
CL1	CE	MET- 364	3.75	0	Hydrophobic	false
F22	SD	MET- 364	3.5	0	Hydrophobic	false
F22	CG	LYS- 367	4.28	0	Hydrophobic	false