scPDB - 2npa entry

Protein Data Bank Entry:

PDB ID : 2npa

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2006-10-26

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 alpha
ID:	PPARA_HUMAN
AC:	Q07869
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:	40.333
Number of residues:	40
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.758	1248.750

% Hydrophobic	% Polar
64.32	35.68
According to VolSite

Ligand :

HET Code:	MMB
Formula:	C25H27N2O5
Molecular weight:	435.492 g/mol
DrugBank ID:	-
Buried Surface Area:	68.15 %
Polar Surface area:	96.98 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	0
Rings:	3
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
36.0751	0.0129063	4.06647

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
C20	CD1	LEU- 247	4.13	0	Hydrophobic	false
C21	CD1	LEU- 254	3.9	0	Hydrophobic	false
C19	CG2	ILE- 272	4.32	0	Hydrophobic	false
C20	CG1	ILE- 272	4.13	0	Hydrophobic	false
C28	CG2	ILE- 272	3.65	0	Hydrophobic	false
C29	CD2	PHE- 273	4.4	0	Hydrophobic	false
C32	CE2	PHE- 273	3.68	0	Hydrophobic	false
C16	CB	CYS- 275	3.55	0	Hydrophobic	false
C2	CB	CYS- 276	4.11	0	Hydrophobic	false
C32	CB	CYS- 276	3.8	0	Hydrophobic	false
C5	SG	CYS- 276	3.81	0	Hydrophobic	false
C9	SG	CYS- 276	3.92	0	Hydrophobic	false
C26	SG	CYS- 276	3.75	0	Hydrophobic	false
C7	CB	CYS- 276	4.06	0	Hydrophobic	false
C32	CG	GLN- 277	3.64	0	Hydrophobic	false
C11	CG2	THR- 279	3.91	0	Hydrophobic	false
C12	CB	THR- 279	4.5	0	Hydrophobic	false
O2	OG	SER- 280	2.88	160.07	H-Bond (Protein Donor)	false
C12	CB	SER- 280	4.4	0	Hydrophobic	false
C2	CB	SER- 280	4.17	0	Hydrophobic	false
C1	CE1	TYR- 314	4.4	0	Hydrophobic	false
O2	OH	TYR- 314	2.53	162.5	H-Bond (Protein Donor)	false
C1	CZ	PHE- 318	4.45	0	Hydrophobic	false
C10	CD2	LEU- 321	3.67	0	Hydrophobic	false
C13	SD	MET- 330	4.24	0	Hydrophobic	false
C5	SD	MET- 330	3.75	0	Hydrophobic	false
C13	CG1	VAL- 332	4.27	0	Hydrophobic	false
C17	CB	VAL- 332	4.09	0	Hydrophobic	false
C18	CG1	VAL- 332	4.06	0	Hydrophobic	false
C19	CD1	ILE- 339	4.09	0	Hydrophobic	false
C5	CG2	ILE- 339	4.25	0	Hydrophobic	false
C28	CD2	LEU- 344	4.12	0	Hydrophobic	false
C5	CD1	LEU- 344	4.33	0	Hydrophobic	false
C28	CD2	LEU- 347	4.44	0	Hydrophobic	false
C26	CG2	ILE- 354	3.52	0	Hydrophobic	false
C29	CD1	ILE- 354	3.61	0	Hydrophobic	false
C8	SD	MET- 355	3.71	0	Hydrophobic	false
C26	SD	MET- 355	3.94	0	Hydrophobic	false
C28	CG	MET- 355	4.15	0	Hydrophobic	false
C5	CG	MET- 355	4.27	0	Hydrophobic	false
C9	CE	MET- 355	3.49	0	Hydrophobic	false
O3	NE2	HIS- 440	2.7	171.31	H-Bond (Protein Donor)	false
O2	OH	TYR- 464	3.37	154.34	H-Bond (Protein Donor)	false