scPDB - 3kdt entry

Protein Data Bank Entry:

PDB ID : 3kdt

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2009-10-23

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
B	100 %

Ligand binding site composition:

B-Factor:	57.904
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.569	637.875

% Hydrophobic	% Polar
60.32	39.68
According to VolSite

Ligand :

HET Code:	7HA
Formula:	C22H20ClN2O6
Molecular weight:	443.857 g/mol
DrugBank ID:	-
Buried Surface Area:	66.8 %
Polar Surface area:	104.93 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:	9

Mass center Coordinates

X	Y	Z
-18.1233	34.5183	12.0435

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
C10	CD1	ILE- 241	4.4	0	Hydrophobic	false
CL13	CB	ALA- 250	4.37	0	Hydrophobic	false
CL13	CG	GLU- 251	4.12	0	Hydrophobic	false
CL13	CG1	VAL- 255	4.09	0	Hydrophobic	false
C1	CG2	ILE- 272	4.49	0	Hydrophobic	false
C8	CG1	ILE- 272	4.37	0	Hydrophobic	false
C31	CE1	PHE- 273	3.67	0	Hydrophobic	false
CL13	SG	CYS- 275	4.3	0	Hydrophobic	false
C9	SG	CYS- 275	3.65	0	Hydrophobic	false
C8	CB	CYS- 275	3.69	0	Hydrophobic	false
C1	CB	CYS- 276	4.5	0	Hydrophobic	false
C14	SG	CYS- 276	4.21	0	Hydrophobic	false
C16	SG	CYS- 276	4.27	0	Hydrophobic	false
C21	CB	CYS- 276	3.89	0	Hydrophobic	false
C31	CG	GLN- 277	4.3	0	Hydrophobic	false
C14	CB	THR- 279	4.38	0	Hydrophobic	false
C17	CG2	THR- 279	4.39	0	Hydrophobic	false
O27	OG	SER- 280	2.51	176.63	H-Bond (Protein Donor)	false
C19	CB	SER- 280	3.95	0	Hydrophobic	false
O26	OH	TYR- 314	3.08	123.26	H-Bond (Protein Donor)	false
C18	CG2	ILE- 317	3.68	0	Hydrophobic	false
C17	CD1	LEU- 321	3.55	0	Hydrophobic	false
C1	SD	MET- 330	3.94	0	Hydrophobic	false
C14	CE	MET- 330	3.79	0	Hydrophobic	false
C16	CE	MET- 330	4.24	0	Hydrophobic	false
C7	CG1	VAL- 332	3.95	0	Hydrophobic	false
C11	CG2	VAL- 332	4.02	0	Hydrophobic	false
C12	CB	VAL- 332	3.49	0	Hydrophobic	false
C14	CG1	VAL- 332	4.4	0	Hydrophobic	false
C8	CD1	ILE- 339	4.13	0	Hydrophobic	false
C1	CG	MET- 355	3.77	0	Hydrophobic	false
C16	CE	MET- 355	4.13	0	Hydrophobic	false
C21	SD	MET- 355	3.83	0	Hydrophobic	false
O26	NE2	HIS- 440	3.08	167.31	H-Bond (Protein Donor)	false
C31	CG2	VAL- 444	3.77	0	Hydrophobic	false
O26	OH	TYR- 464	3.33	151.62	H-Bond (Protein Donor)	false