scPDB - 1knu entry

Protein Data Bank Entry:

PDB ID : 1knu

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2001-12-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	6.770	6.770	6.770	0.000	6.770	1

List of CHEMBLId :

CHEMBL86658

Binding Site :

Uniprot Annotation

Name:	Peroxisome proliferator-activated receptor gamma
ID:	PPARG_HUMAN
AC:	P37231
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:	56.298
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.697	1194.750

% Hydrophobic	% Polar
68.08	31.92
According to VolSite

Ligand :

HET Code:	YPA
Formula:	C25H24NO4
Molecular weight:	402.462 g/mol
DrugBank ID:	DB04270
Buried Surface Area:	62.3 %
Polar Surface area:	63.52 Å2

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

Mass center Coordinates

X	Y	Z
16.7126	64.1522	13.2198

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
C50	CE1	PHE- 282	3.4	0	Hydrophobic	false
C17	SG	CYS- 285	4.29	0	Hydrophobic	false
C22	SG	CYS- 285	3.62	0	Hydrophobic	false
C30	SG	CYS- 285	3.56	0	Hydrophobic	false
C50	CB	CYS- 285	3.5	0	Hydrophobic	false
C34	CB	CYS- 285	3.91	0	Hydrophobic	false
C50	CG	GLN- 286	3.68	0	Hydrophobic	false
C5	CG	ARG- 288	3.2	0	Hydrophobic	false
C1	CD	ARG- 288	3.38	0	Hydrophobic	false
C40	CB	SER- 289	3.72	0	Hydrophobic	false
C33	CB	SER- 289	3.89	0	Hydrophobic	false
O45	OG	SER- 289	2.8	167.56	H-Bond (Protein Donor)	false
O45	NE2	HIS- 323	2.97	151.81	H-Bond (Protein Donor)	false
C33	CG2	ILE- 326	4.06	0	Hydrophobic	false
C39	CE1	TYR- 327	4.02	0	Hydrophobic	false
C23	CD1	LEU- 330	4.15	0	Hydrophobic	false
C29	CD2	LEU- 330	4.29	0	Hydrophobic	false
C6	CD1	LEU- 333	4.31	0	Hydrophobic	false
C4	CG2	ILE- 341	3.97	0	Hydrophobic	false
C15	CD1	ILE- 341	4.42	0	Hydrophobic	false
C22	CG2	ILE- 341	4.42	0	Hydrophobic	false
C12	CG2	ILE- 341	3.72	0	Hydrophobic	false
C11	CB	ILE- 341	3.6	0	Hydrophobic	false
C29	CE	MET- 364	4.1	0	Hydrophobic	false
C30	SD	MET- 364	3.48	0	Hydrophobic	false
O44	NE2	HIS- 449	2.87	129.46	H-Bond (Protein Donor)	false
O47	NE2	HIS- 449	3.2	121.94	H-Bond (Protein Donor)	false
O44	OH	TYR- 473	2.91	148.3	H-Bond (Protein Donor)	false