scPDB - 4k6i entry

Protein Data Bank Entry:

PDB ID : 4k6i

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2013-04-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	5.720	7.300	7.520	0.710	7.850	12

List of CHEMBLId :

CHEMBL1023

Binding Site :

Uniprot Annotation

Name:	Retinoic acid receptor RXR-alpha
ID:	RXRA_HUMAN
AC:	P19793
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:	35.903
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.981	438.750

% Hydrophobic	% Polar
80.00	20.00
According to VolSite

Ligand :

HET Code:	9RA
Formula:	C24H27O2
Molecular weight:	347.470 g/mol
DrugBank ID:	DB00307
Buried Surface Area:	71.74 %
Polar Surface area:	40.12 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	0
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
-2.89365	19.1697	-3.72412

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
C39	CG1	VAL- 265	4.28	0	Hydrophobic	false
C31	CD1	ILE- 268	4.33	0	Hydrophobic	false
C21	CD1	ILE- 268	4.41	0	Hydrophobic	false
C9	CG2	ILE- 268	3.33	0	Hydrophobic	false
C3	CG2	ILE- 268	3.47	0	Hydrophobic	false
C39	CG2	ILE- 268	4.22	0	Hydrophobic	false
C2	CG2	ILE- 268	3.47	0	Hydrophobic	false
C11	CB	ALA- 271	4.34	0	Hydrophobic	false
C43	CB	ALA- 272	3.43	0	Hydrophobic	false
C13	CB	ALA- 272	3.8	0	Hydrophobic	false
C13	CB	LEU- 309	3.45	0	Hydrophobic	false
C27	CZ	PHE- 313	4.33	0	Hydrophobic	false
C31	CZ	PHE- 313	4.19	0	Hydrophobic	false
C9	CE2	PHE- 313	3.37	0	Hydrophobic	false
C11	CB	PHE- 313	4.11	0	Hydrophobic	false
O53	CZ	ARG- 316	3.65	0	Ionic (Protein Cationic)	false
O53	NH2	ARG- 316	3.28	142.36	H-Bond (Protein Donor)	false
O53	NH1	ARG- 316	3.14	149.23	H-Bond (Protein Donor)	false
O52	NH1	ARG- 316	3.4	152.18	H-Bond (Protein Donor)	false
C10	CD2	LEU- 326	4.08	0	Hydrophobic	false
O52	N	ALA- 327	2.97	158.68	H-Bond (Protein Donor)	false
C21	CG2	VAL- 342	4.03	0	Hydrophobic	false
C27	CG1	ILE- 345	4.26	0	Hydrophobic	false
C20	CG2	ILE- 345	3.57	0	Hydrophobic	false
C31	CD1	PHE- 346	3.91	0	Hydrophobic	false
C27	CG2	VAL- 349	3.72	0	Hydrophobic	false
C27	SG	CYS- 432	4.38	0	Hydrophobic	false
C35	SG	CYS- 432	4.34	0	Hydrophobic	false
C2	SG	CYS- 432	3.76	0	Hydrophobic	false
C35	CB	HIS- 435	3.75	0	Hydrophobic	false
C43	CD2	LEU- 436	4.03	0	Hydrophobic	false
C39	CE1	PHE- 439	3.92	0	Hydrophobic	false
C35	CE1	PHE- 439	4.17	0	Hydrophobic	false