scPDB - 3sp9 entry

Protein Data Bank Entry:

PDB ID : 3sp9

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2011-07-01

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:	15.393
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.832	772.875

% Hydrophobic	% Polar
62.88	37.12
According to VolSite

Ligand :

HET Code:	IL2
Formula:	C22H31O4
Molecular weight:	359.479 g/mol
DrugBank ID:	-
Buried Surface Area:	66.69 %
Polar Surface area:	80.59 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
25.1367	-0.614846	3.08269

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
C22	CD1	LEU- 219	3.75	0	Hydrophobic	false
C22	CG2	VAL- 245	4.12	0	Hydrophobic	false
C21	CG1	VAL- 245	4.03	0	Hydrophobic	false
C14	CE1	PHE- 246	3.38	0	Hydrophobic	false
C18	CB	ARG- 248	3.7	0	Hydrophobic	false
C22	CG	ARG- 248	3.88	0	Hydrophobic	false
C21	CB	ARG- 248	3.93	0	Hydrophobic	false
C6	SG	CYS- 249	4.05	0	Hydrophobic	false
C14	CB	CYS- 249	4.31	0	Hydrophobic	false
C15	SG	CYS- 249	3.84	0	Hydrophobic	false
C16	CG	GLN- 250	4.16	0	Hydrophobic	false
O2	OG1	THR- 252	2.88	152.96	H-Bond (Ligand Donor)	false
C13	CB	THR- 252	4.37	0	Hydrophobic	false
O1	OG1	THR- 253	2.96	158.72	H-Bond (Ligand Donor)	false
O4	OG1	THR- 253	2.64	161.39	H-Bond (Protein Donor)	false
C16	CB	THR- 253	4.2	0	Hydrophobic	false
O3	NE2	HIS- 287	2.95	145.58	H-Bond (Protein Donor)	false
O4	NE2	HIS- 287	3.33	137.66	H-Bond (Protein Donor)	false
C4	CG2	ILE- 290	3.67	0	Hydrophobic	false
C4	CE1	PHE- 291	3.9	0	Hydrophobic	false
C5	CD1	LEU- 294	4.43	0	Hydrophobic	false
C2	CD2	LEU- 294	4.41	0	Hydrophobic	false
C13	CD1	LEU- 303	3.73	0	Hydrophobic	false
C17	CG1	VAL- 305	4.11	0	Hydrophobic	false
C21	CG2	VAL- 312	3.75	0	Hydrophobic	false
C17	CD2	LEU- 317	4.39	0	Hydrophobic	false
C12	CG2	ILE- 327	4.17	0	Hydrophobic	false
C6	CG1	ILE- 328	3.89	0	Hydrophobic	false
C2	CG	LYS- 331	4.4	0	Hydrophobic	false
O3	NE2	HIS- 413	2.74	146.72	H-Bond (Protein Donor)	false
C16	CD1	LEU- 433	4.1	0	Hydrophobic	false
O3	OH	TYR- 437	2.67	160.36	H-Bond (Protein Donor)	false