scPDB - 3gbk entry

Protein Data Bank Entry:

PDB ID : 3gbk

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2009-02-19

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:	44.500
Number of residues:	43
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.593	877.500

% Hydrophobic	% Polar
65.77	34.23
According to VolSite

Ligand :

HET Code:	2PQ
Formula:	C38H40NO5
Molecular weight:	590.728 g/mol
DrugBank ID:	-
Buried Surface Area:	69.13 %
Polar Surface area:	78.9 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	0
Rings:	5
Aromatic rings:	4
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
36.5965	-5.81245	38.9653

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
CAD	CD1	LEU- 255	3.64	0	Hydrophobic	false
CAD	CG	GLU- 259	3.29	0	Hydrophobic	false
CAI	CD2	LEU- 270	4.36	0	Hydrophobic	false
CAZ	CD1	PHE- 282	4.16	0	Hydrophobic	false
CBA	CE1	PHE- 282	3.63	0	Hydrophobic	false
CBF	CZ	PHE- 282	3.35	0	Hydrophobic	false
CAL	SG	CYS- 285	4.25	0	Hydrophobic	false
CAZ	SG	CYS- 285	3.87	0	Hydrophobic	false
CBG	CB	CYS- 285	4.46	0	Hydrophobic	false
CBA	CB	CYS- 285	4.16	0	Hydrophobic	false
CAM	SG	CYS- 285	3.92	0	Hydrophobic	false
CBF	CG	GLN- 286	4.05	0	Hydrophobic	false
CBG	CG	GLN- 286	3.62	0	Hydrophobic	false
CAO	CG	ARG- 288	3.89	0	Hydrophobic	false
CBN	CG	ARG- 288	3.78	0	Hydrophobic	false
CBG	CB	SER- 289	4.06	0	Hydrophobic	false
CBO	CB	SER- 289	3.96	0	Hydrophobic	false
CAS	CB	SER- 289	4.09	0	Hydrophobic	false
OBC	OG	SER- 289	2.97	162.17	H-Bond (Protein Donor)	false
OBC	NE2	HIS- 323	2.97	147.45	H-Bond (Protein Donor)	false
CBO	CG2	ILE- 326	3.32	0	Hydrophobic	false
CAT	CG2	ILE- 326	4.14	0	Hydrophobic	false
CBH	CD2	LEU- 330	4.25	0	Hydrophobic	false
CBI	CD2	LEU- 330	3.41	0	Hydrophobic	false
CBM	CD1	LEU- 330	3.77	0	Hydrophobic	false
CBK	CE	MET- 334	4.36	0	Hydrophobic	false
CAR	CG1	VAL- 339	4.12	0	Hydrophobic	false
CBK	CG1	VAL- 339	4.43	0	Hydrophobic	false
CAI	CD1	ILE- 341	4.16	0	Hydrophobic	false
CAH	CB	ILE- 341	4.16	0	Hydrophobic	false
CAG	CG2	ILE- 341	4.17	0	Hydrophobic	false
CAQ	CG2	ILE- 341	3.25	0	Hydrophobic	false
CAK	CE	MET- 348	4.31	0	Hydrophobic	false
CBK	CD1	LEU- 353	4.43	0	Hydrophobic	false
CBA	CD1	PHE- 363	3.89	0	Hydrophobic	false
CAY	CB	PHE- 363	3.7	0	Hydrophobic	false
CAY	SD	MET- 364	3.69	0	Hydrophobic	false
CAZ	CE	MET- 364	3.9	0	Hydrophobic	false
CBJ	SD	MET- 364	3.67	0	Hydrophobic	false
CBJ	CB	LYS- 367	4.43	0	Hydrophobic	false
CBI	CG	LYS- 367	4.16	0	Hydrophobic	false
OBE	NE2	HIS- 449	3.34	126.97	H-Bond (Protein Donor)	false
OBR	NE2	HIS- 449	2.88	143.81	H-Bond (Protein Donor)	false
CBF	CD1	LEU- 453	4.32	0	Hydrophobic	false
CBF	CD2	LEU- 465	3.93	0	Hydrophobic	false
CBG	CD1	LEU- 469	4.01	0	Hydrophobic	false
OBR	OH	TYR- 473	2.7	127.61	H-Bond (Protein Donor)	false