scPDB - 1y0s entry

Protein Data Bank Entry:

PDB ID : 1y0s

Resolution :2.650 Å

Experimental Method : X-ray

Deposition Date : 2004-11-16

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 delta
ID:	PPARD_HUMAN
AC:	Q03181
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:	39.640
Number of residues:	45
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	IOD

Cavity properties

Ligandability	Volume (Å3)
1.626	1231.875

% Hydrophobic	% Polar
56.44	43.56
According to VolSite

Ligand :

HET Code:	331
Formula:	C27H35F2N2O4
Molecular weight:	489.575 g/mol
DrugBank ID:	-
Buried Surface Area:	64.31 %
Polar Surface area:	81.7 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:	1
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
31.3035	8.0016	59.2609

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
C28	CD1	ILE- 249	4.22	0	Hydrophobic	false
C26	CH2	TRP- 264	3.9	0	Hydrophobic	false
C24	CG1	VAL- 281	3.74	0	Hydrophobic	false
C32	CZ	PHE- 282	4.15	0	Hydrophobic	false
C26	CB	ARG- 284	4.05	0	Hydrophobic	false
C12	SG	CYS- 285	4.1	0	Hydrophobic	false
C17	CB	CYS- 285	4.32	0	Hydrophobic	false
C19	SG	CYS- 285	3.56	0	Hydrophobic	false
C22	CB	CYS- 285	3.75	0	Hydrophobic	false
C35	CB	CYS- 285	4.37	0	Hydrophobic	false
C18	SG	CYS- 285	3.74	0	Hydrophobic	false
C31	CG	GLN- 286	3.58	0	Hydrophobic	false
C4	CG2	THR- 288	3.42	0	Hydrophobic	false
C35	CG2	THR- 289	3.59	0	Hydrophobic	false
F14	CG2	THR- 292	4.27	0	Hydrophobic	false
O33	NE2	HIS- 323	2.84	174.35	H-Bond (Protein Donor)	false
F7	CB	ILE- 326	4.27	0	Hydrophobic	false
C3	CG2	ILE- 326	3.62	0	Hydrophobic	false
F14	CB	MET- 329	3.34	0	Hydrophobic	false
C3	CD1	LEU- 330	3.53	0	Hydrophobic	false
C4	CD1	LEU- 330	4.49	0	Hydrophobic	false
C6	CB	LEU- 330	3.95	0	Hydrophobic	false
F7	CB	LEU- 330	3.37	0	Hydrophobic	false
C4	CD1	ILE- 333	3.69	0	Hydrophobic	false
C13	CD1	LEU- 339	3.89	0	Hydrophobic	false
C21	CG1	VAL- 341	4.07	0	Hydrophobic	false
C28	CG2	VAL- 348	3.84	0	Hydrophobic	false
C22	CD1	ILE- 363	3.27	0	Hydrophobic	false
C13	CD1	ILE- 364	4.14	0	Hydrophobic	false
O27	NE2	HIS- 449	3.1	129.99	H-Bond (Protein Donor)	false
O34	NE2	HIS- 449	2.73	149.23	H-Bond (Protein Donor)	false
C32	SD	MET- 453	3.4	0	Hydrophobic	false
C32	CD1	LEU- 469	4.36	0	Hydrophobic	false
C35	CD1	LEU- 469	3.74	0	Hydrophobic	false
C32	CE2	TYR- 473	4.29	0	Hydrophobic	false
O34	OH	TYR- 473	2.63	150.05	H-Bond (Protein Donor)	false