scPDB - 4a4v entry

Protein Data Bank Entry:

PDB ID : 4a4v

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2011-10-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	6.540	6.540	6.540	0.000	6.540	1

List of CHEMBLId :

CHEMBL2337126

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
B	100 %

Ligand binding site composition:

B-Factor:	39.222
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.525	1117.125

% Hydrophobic	% Polar
60.12	39.88
According to VolSite

Ligand :

HET Code:	YFD
Formula:	C18H25O4
Molecular weight:	305.389 g/mol
DrugBank ID:	-
Buried Surface Area:	63.79 %
Polar Surface area:	69.59 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
1.49005	-9.65	-18.3101

Binding mode :

What is Poseview ?

2D View
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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
CAA	CE1	PHE- 226	4.43	0	Hydrophobic	false
CAD	CG2	ILE- 281	4.4	0	Hydrophobic	false
CAC	CG2	ILE- 281	4.39	0	Hydrophobic	false
CAT	SG	CYS- 285	4.08	0	Hydrophobic	false
CAB	SG	CYS- 285	3.66	0	Hydrophobic	false
CAK	SG	CYS- 285	4.44	0	Hydrophobic	false
CAC	CB	CYS- 285	4.21	0	Hydrophobic	false
OAE	NH2	ARG- 288	3.22	129.6	H-Bond (Protein Donor)	false
OAE	NE	ARG- 288	2.61	170.8	H-Bond (Protein Donor)	false
OAE	CZ	ARG- 288	3.34	0	Ionic (Protein Cationic)	false
CAV	CG	ARG- 288	3.44	0	Hydrophobic	false
CAN	CB	ALA- 292	4.08	0	Hydrophobic	false
CAA	CB	ALA- 292	3.67	0	Hydrophobic	false
CAA	CD1	ILE- 296	3.86	0	Hydrophobic	false
CAA	CG1	ILE- 326	4.36	0	Hydrophobic	false
CAL	CG2	ILE- 326	4.18	0	Hydrophobic	false
CAI	CG2	ILE- 326	4.41	0	Hydrophobic	false
CAB	CG2	ILE- 326	3.67	0	Hydrophobic	false
CAB	CE1	TYR- 327	4.01	0	Hydrophobic	false
CAA	SD	MET- 329	3.33	0	Hydrophobic	false
CAJ	CB	MET- 329	3.69	0	Hydrophobic	false
CAM	CB	LEU- 330	4.49	0	Hydrophobic	false
CAB	CD2	LEU- 330	3.62	0	Hydrophobic	false
CAK	CD1	LEU- 330	4.02	0	Hydrophobic	false
CAU	CD1	LEU- 330	3.43	0	Hydrophobic	false
CAM	CD1	LEU- 333	4.37	0	Hydrophobic	false
CAV	CD1	LEU- 333	4.07	0	Hydrophobic	false
CAK	CG2	VAL- 339	4.39	0	Hydrophobic	false
CAK	CG2	ILE- 341	4.44	0	Hydrophobic	false
CAC	CG2	ILE- 341	4.41	0	Hydrophobic	false
CAD	SD	MET- 348	4.46	0	Hydrophobic	false
CAD	CD2	LEU- 353	4.24	0	Hydrophobic	false
CAD	CG	MET- 364	4.29	0	Hydrophobic	false