scPDB - 3d5f entry

Protein Data Bank Entry:

PDB ID : 3d5f

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2008-05-16

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:	32.438
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
2.444	519.750

% Hydrophobic	% Polar
83.12	16.88
According to VolSite

Ligand :

HET Code:	L41
Formula:	C22H25O7
Molecular weight:	401.430 g/mol
DrugBank ID:	DB08078
Buried Surface Area:	70.69 %
Polar Surface area:	105.12 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
33.0802	6.47962	58.3164

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
C15	CH2	TRP- 264	4.07	0	Hydrophobic	false
C10	CG1	VAL- 281	4.08	0	Hydrophobic	false
C15	CG1	VAL- 281	4.31	0	Hydrophobic	false
C7	CB	ARG- 284	4.47	0	Hydrophobic	false
C15	CB	ARG- 284	3.83	0	Hydrophobic	false
C9	CB	CYS- 285	4.19	0	Hydrophobic	false
C11	SG	CYS- 285	4.39	0	Hydrophobic	false
C20	SG	CYS- 285	3.86	0	Hydrophobic	false
C23	CB	CYS- 285	3.91	0	Hydrophobic	false
C24	CB	CYS- 285	3.74	0	Hydrophobic	false
C5	SG	CYS- 285	3.57	0	Hydrophobic	false
C26	CG	GLN- 286	4.04	0	Hydrophobic	false
C3	CB	THR- 288	4.44	0	Hydrophobic	false
C9	CG2	THR- 288	3.84	0	Hydrophobic	false
C26	CG2	THR- 289	3.92	0	Hydrophobic	false
C13	CG2	THR- 289	3.63	0	Hydrophobic	false
C23	CG2	THR- 289	3.65	0	Hydrophobic	false
O28	OG1	THR- 289	3.36	155.95	H-Bond (Protein Donor)	false
O28	NE2	HIS- 323	2.66	174.63	H-Bond (Protein Donor)	false
O29	NE2	HIS- 323	3.32	125.31	H-Bond (Protein Donor)	false
C13	CG2	ILE- 326	4.2	0	Hydrophobic	false
C4	CD2	LEU- 330	4.49	0	Hydrophobic	false
C13	CD1	LEU- 330	4.24	0	Hydrophobic	false
C14	CD1	LEU- 330	3.54	0	Hydrophobic	false
C5	CD2	LEU- 339	4.27	0	Hydrophobic	false
C11	CD1	LEU- 339	4.18	0	Hydrophobic	false
C2	CD1	LEU- 339	3.74	0	Hydrophobic	false
C15	CG1	VAL- 341	4.05	0	Hydrophobic	false
C7	CG1	VAL- 341	3.72	0	Hydrophobic	false
C15	CG2	VAL- 348	3.99	0	Hydrophobic	false
C20	CG2	ILE- 363	3.96	0	Hydrophobic	false
C11	CG2	ILE- 364	3.73	0	Hydrophobic	false
C20	CG1	ILE- 364	3.97	0	Hydrophobic	false
C14	CB	LYS- 367	3.91	0	Hydrophobic	false
C17	CG	LYS- 367	3.74	0	Hydrophobic	false
O29	NE2	HIS- 449	2.75	159.61	H-Bond (Protein Donor)	false
C26	SD	MET- 453	4.47	0	Hydrophobic	false
C22	CE	MET- 453	4.02	0	Hydrophobic	false
C26	CD2	LEU- 469	4.01	0	Hydrophobic	false
O29	OH	TYR- 473	2.91	150.03	H-Bond (Protein Donor)	false