scPDB - 1kkq entry

Protein Data Bank Entry:

PDB ID : 1kkq

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2001-12-10

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	98 %
E	2 %

Ligand binding site composition:

B-Factor:	57.761
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.816	1066.500

% Hydrophobic	% Polar
67.41	32.59
According to VolSite

Ligand :

HET Code:	471
Formula:	C35H37F3N3O4
Molecular weight:	620.681 g/mol
DrugBank ID:	-
Buried Surface Area:	57.5 %
Polar Surface area:	98.04 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
76.3225	27.983	23.9525

Binding mode :

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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
C3K	CD1	ILE- 241	4.03	0	Hydrophobic	false
C3K	CD1	LEU- 247	4.05	0	Hydrophobic	false
C3L	CB	ALA- 250	4.35	0	Hydrophobic	false
C3N	CD2	LEU- 254	4.12	0	Hydrophobic	false
C3M	CD1	LEU- 254	4.32	0	Hydrophobic	false
C3L	CD2	LEU- 254	3.57	0	Hydrophobic	false
F1O	CG2	ILE- 272	3.31	0	Hydrophobic	false
C3J	CG2	ILE- 272	4.27	0	Hydrophobic	false
F1Q	CB	ILE- 272	4.08	0	Hydrophobic	false
C1J	CB	PHE- 273	3.67	0	Hydrophobic	false
C3N	CB	CYS- 275	3.55	0	Hydrophobic	false
C3K	SG	CYS- 275	3.33	0	Hydrophobic	false
C1B	CB	CYS- 276	4.19	0	Hydrophobic	false
C3E	SG	CYS- 276	3.73	0	Hydrophobic	false
C1M	SG	CYS- 276	4.2	0	Hydrophobic	false
C3A	SG	CYS- 276	3.58	0	Hydrophobic	false
C1B	CG	GLN- 277	3.7	0	Hydrophobic	false
CD2	CB	SER- 280	4.31	0	Hydrophobic	false
N4B	OH	TYR- 314	3.34	124.36	H-Bond (Ligand Donor)	false
CB	CE1	TYR- 314	4.12	0	Hydrophobic	false
CD2	CG2	ILE- 317	4.32	0	Hydrophobic	false
C3E	SD	MET- 330	4.21	0	Hydrophobic	false
C3B	CE	MET- 330	4.13	0	Hydrophobic	false
C3M	CG2	VAL- 332	4.4	0	Hydrophobic	false
C3B	CG1	VAL- 332	4.34	0	Hydrophobic	false
C3N	CB	VAL- 332	3.75	0	Hydrophobic	false
F1O	CD2	LEU- 344	4.43	0	Hydrophobic	false
C3E	CD2	LEU- 344	4.21	0	Hydrophobic	false
F1O	CD1	LEU- 347	3.76	0	Hydrophobic	false
F1P	CB	PHE- 351	3.91	0	Hydrophobic	false
F1Q	CD1	PHE- 351	3.33	0	Hydrophobic	false
C1M	CG2	ILE- 354	4.05	0	Hydrophobic	false
C1K	CD1	ILE- 354	3.63	0	Hydrophobic	false
CE1	CE	MET- 355	4.31	0	Hydrophobic	false
C1M	SD	MET- 355	4.36	0	Hydrophobic	false
C3E	SD	MET- 355	4.5	0	Hydrophobic	false
C4E	CD1	LEU- 456	3.36	0	Hydrophobic	false