scPDB - 2p1t entry

Protein Data Bank Entry:

PDB ID : 2p1t

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2007-03-06

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:	12.433
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.294	675.000

% Hydrophobic	% Polar
63.00	37.00
According to VolSite

Ligand :

HET Code:	3TN
Formula:	C24H27O4
Molecular weight:	379.469 g/mol
DrugBank ID:	-
Buried Surface Area:	74.96 %
Polar Surface area:	69.59 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
-3.22004	-18.435	31.5891

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
CAB	CG2	VAL- 265	4.11	0	Hydrophobic	false
CAA	CG2	ILE- 268	3.99	0	Hydrophobic	false
CAB	CD1	ILE- 268	4.25	0	Hydrophobic	false
CAQ	CD1	ILE- 268	4.3	0	Hydrophobic	false
CAE	CD1	ILE- 268	4.08	0	Hydrophobic	false
CAO	CG2	ILE- 268	3.5	0	Hydrophobic	false
CAX	CG2	ILE- 268	3.4	0	Hydrophobic	false
CAA	SG	CYS- 269	3.65	0	Hydrophobic	false
CAA	CB	ALA- 272	4.4	0	Hydrophobic	false
CAK	CB	ALA- 272	3.67	0	Hydrophobic	false
OAH	OD1	ASN- 306	2.55	166.27	H-Bond (Ligand Donor)	false
CAK	CB	LEU- 309	3.61	0	Hydrophobic	false
CAU	CG1	ILE- 310	4.29	0	Hydrophobic	false
CAD	CZ	PHE- 313	4.23	0	Hydrophobic	false
CAE	CZ	PHE- 313	4.24	0	Hydrophobic	false
CAM	CE2	PHE- 313	3.42	0	Hydrophobic	false
OAG	NH2	ARG- 316	3.1	143.01	H-Bond (Protein Donor)	false
OAG	NH1	ARG- 316	2.96	151.09	H-Bond (Protein Donor)	false
OAG	CZ	ARG- 316	3.47	0	Ionic (Protein Cationic)	false
CAE	CD1	ILE- 324	3.38	0	Hydrophobic	false
OAF	N	ALA- 327	2.87	161.58	H-Bond (Protein Donor)	false
CAB	CG2	VAL- 342	4.09	0	Hydrophobic	false
CAP	CB	VAL- 342	4.13	0	Hydrophobic	false
CAC	CG2	ILE- 345	4.13	0	Hydrophobic	false
CAP	CG2	ILE- 345	3.55	0	Hydrophobic	false
CAE	CD1	PHE- 346	3.87	0	Hydrophobic	false
CAD	CG2	VAL- 349	3.71	0	Hydrophobic	false
CAD	SG	CYS- 432	3.77	0	Hydrophobic	false
CAZ	SG	CYS- 432	4.25	0	Hydrophobic	false
CAC	CB	HIS- 435	3.43	0	Hydrophobic	false
CAA	CD1	LEU- 436	4.16	0	Hydrophobic	false
CAB	CZ	PHE- 439	3.91	0	Hydrophobic	false
CAC	CZ	PHE- 439	4.13	0	Hydrophobic	false
OAR	O	HOH- 480	2.97	179.95	H-Bond (Protein Donor)	false