scPDB - 2yfe entry

Protein Data Bank Entry:

PDB ID : 2yfe

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2011-04-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	6.630	6.630	6.630	0.000	6.630	1

List of CHEMBLId :

CHEMBL491820

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
B	100 %

Ligand binding site composition:

B-Factor:	41.687
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.496	1103.625

% Hydrophobic	% Polar
61.47	38.53
According to VolSite

Ligand :

HET Code:	YFE
Formula:	C21H23O4
Molecular weight:	339.405 g/mol
DrugBank ID:	-
Buried Surface Area:	64.42 %
Polar Surface area:	69.59 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:	7

Mass center Coordinates

X	Y	Z
-1.346	-10.2926	18.8611

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
CAB	CG2	ILE- 281	4.07	0	Hydrophobic	false
CAB	CB	CYS- 285	3.46	0	Hydrophobic	false
CAW	SG	CYS- 285	4.24	0	Hydrophobic	false
CAA	SG	CYS- 285	3.48	0	Hydrophobic	false
OAD	NH2	ARG- 288	3.25	129.05	H-Bond (Protein Donor)	false
OAD	NE	ARG- 288	2.65	163.18	H-Bond (Protein Donor)	false
OAD	CZ	ARG- 288	3.37	0	Ionic (Protein Cationic)	false
CAY	CG	ARG- 288	3.33	0	Hydrophobic	false
CAV	CG	ARG- 288	3.59	0	Hydrophobic	false
CAP	CB	ALA- 292	4.06	0	Hydrophobic	false
CAK	CB	ALA- 292	3.54	0	Hydrophobic	false
CAI	CD1	ILE- 296	3.87	0	Hydrophobic	false
CAH	CG1	ILE- 296	4.26	0	Hydrophobic	false
CAM	CG2	ILE- 326	4.4	0	Hydrophobic	false
CAA	CG2	ILE- 326	4.15	0	Hydrophobic	false
CAK	CG1	ILE- 326	3.92	0	Hydrophobic	false
CAA	CE1	TYR- 327	4.05	0	Hydrophobic	false
CAH	CG	MET- 329	3.59	0	Hydrophobic	false
CAI	CB	MET- 329	3.5	0	Hydrophobic	false
CAA	CD2	LEU- 330	3.71	0	Hydrophobic	false
CAX	CD1	LEU- 330	3.47	0	Hydrophobic	false
CAY	CD1	LEU- 333	4.29	0	Hydrophobic	false
CAO	CD1	LEU- 333	4.3	0	Hydrophobic	false
CAN	CG2	VAL- 339	4.46	0	Hydrophobic	false
CAC	CG2	ILE- 341	3.86	0	Hydrophobic	false
CAN	CG2	ILE- 341	4.27	0	Hydrophobic	false
CAB	CD2	LEU- 353	4.44	0	Hydrophobic	false
CAB	CZ	PHE- 363	3.44	0	Hydrophobic	false
CAB	SD	MET- 364	3.91	0	Hydrophobic	false
CAN	CE	MET- 364	4.33	0	Hydrophobic	false