scPDB - 1nyx entry

Protein Data Bank Entry:

PDB ID : 1nyx

Resolution :2.650 Å

Experimental Method : X-ray

Deposition Date : 2003-02-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.050	7.050	7.050	0.000	7.050	1

List of CHEMBLId :

CHEMBL24038

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:	43.414
Number of residues:	38
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.550	1218.375

% Hydrophobic	% Polar
63.43	36.57
According to VolSite

Ligand :

HET Code:	DRF
Formula:	C25H24NO5
Molecular weight:	418.462 g/mol
DrugBank ID:	DB07675
Buried Surface Area:	63.94 %
Polar Surface area:	71.06 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	0
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
17.0292	63.4349	13.4589

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
C6	CG2	ILE- 281	3.47	0	Hydrophobic	false
C49	CD1	PHE- 282	3.63	0	Hydrophobic	false
C49	CB	CYS- 285	3.92	0	Hydrophobic	false
C30	SG	CYS- 285	3.33	0	Hydrophobic	false
C24	SG	CYS- 285	3.22	0	Hydrophobic	false
C35	SG	CYS- 285	3.59	0	Hydrophobic	false
C2	SG	CYS- 285	3.51	0	Hydrophobic	false
C48	CG	GLN- 286	4.03	0	Hydrophobic	false
C49	CB	GLN- 286	4.25	0	Hydrophobic	false
C24	CG	ARG- 288	4.18	0	Hydrophobic	false
C12	CG	ARG- 288	3.72	0	Hydrophobic	false
C16	CB	ARG- 288	3.87	0	Hydrophobic	false
C13	CD	ARG- 288	3.69	0	Hydrophobic	false
C40	CB	SER- 289	3.87	0	Hydrophobic	false
C32	CB	SER- 289	3.26	0	Hydrophobic	false
O45	NE2	HIS- 323	2.57	160.1	H-Bond (Protein Donor)	false
C32	CG2	ILE- 326	3.62	0	Hydrophobic	false
C40	CE1	TYR- 327	4.49	0	Hydrophobic	false
C35	CD2	LEU- 330	4.27	0	Hydrophobic	false
C30	CD1	LEU- 330	3.88	0	Hydrophobic	false
C24	CD1	LEU- 330	3.91	0	Hydrophobic	false
C4	CB	ILE- 341	4.31	0	Hydrophobic	false
C3	CG2	ILE- 341	4.12	0	Hydrophobic	false
C16	CB	ILE- 341	3.98	0	Hydrophobic	false
C1	SD	MET- 348	3.94	0	Hydrophobic	false
C1	CD2	LEU- 353	4.46	0	Hydrophobic	false
C35	SD	MET- 364	3.97	0	Hydrophobic	false
O46	NE2	HIS- 449	3.22	120.54	H-Bond (Protein Donor)	false
O55	OH	TYR- 473	2.84	163.19	H-Bond (Protein Donor)	false