scPDB - 3fc6 entry

Protein Data Bank Entry:

PDB ID : 3fc6

Resolution :2.060 Å

Experimental Method : X-ray

Deposition Date : 2008-11-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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:	38.345
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.589	681.750

% Hydrophobic	% Polar
64.36	35.64
According to VolSite

Ligand :

HET Code:	REA
Formula:	C20H27O2
Molecular weight:	299.427 g/mol
DrugBank ID:	DB00755
Buried Surface Area:	60.56 %
Polar Surface area:	40.12 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	0
Rings:	1
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
85.6931	59.3777	35.3546

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
C2	CG2	VAL- 265	4.49	0	Hydrophobic	false
C16	CG1	VAL- 265	4.4	0	Hydrophobic	false
C11	CG2	ILE- 268	3.91	0	Hydrophobic	false
C16	CG2	ILE- 268	4.27	0	Hydrophobic	false
C20	CG2	ILE- 268	4.03	0	Hydrophobic	false
C3	CD1	ILE- 268	3.86	0	Hydrophobic	false
C7	CG2	ILE- 268	3.81	0	Hydrophobic	false
C16	SG	CYS- 269	4.24	0	Hydrophobic	false
C20	CB	ALA- 271	3.58	0	Hydrophobic	false
C12	CB	ALA- 272	3.27	0	Hydrophobic	false
C10	CB	LEU- 309	4.43	0	Hydrophobic	false
C12	CB	LEU- 309	4.03	0	Hydrophobic	false
C8	CG1	ILE- 310	4.32	0	Hydrophobic	false
C10	CG1	ILE- 310	4.17	0	Hydrophobic	false
C12	CD2	PHE- 313	3.97	0	Hydrophobic	false
C18	CZ	PHE- 313	3.8	0	Hydrophobic	false
C20	CD2	PHE- 313	3.57	0	Hydrophobic	false
C11	CE2	PHE- 313	3.9	0	Hydrophobic	false
O1	CZ	ARG- 316	3.18	0	Ionic (Protein Cationic)	false
O1	NH1	ARG- 316	2.78	141.64	H-Bond (Protein Donor)	false
O1	NH2	ARG- 316	2.74	143.85	H-Bond (Protein Donor)	false
O2	NH1	ARG- 316	3.31	156.68	H-Bond (Protein Donor)	false
C20	CD2	LEU- 326	4.01	0	Hydrophobic	false
O2	N	ALA- 327	2.77	141.82	H-Bond (Protein Donor)	false
C2	CG1	VAL- 342	4.2	0	Hydrophobic	false
C3	CG2	VAL- 342	4.06	0	Hydrophobic	false
C4	CG2	ILE- 345	3.8	0	Hydrophobic	false
C4	SG	CYS- 432	4.3	0	Hydrophobic	false
C17	SG	CYS- 432	4.08	0	Hydrophobic	false
C18	SG	CYS- 432	3.83	0	Hydrophobic	false
C8	SG	CYS- 432	4.23	0	Hydrophobic	false