scPDB - 2p1v entry

Protein Data Bank Entry:

PDB ID : 2p1v

Resolution :2.200 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:	25.924
Number of residues:	36
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
2.019	486.000

% Hydrophobic	% Polar
76.39	23.61
According to VolSite

Ligand :

HET Code:	5TN
Formula:	C26H31O4
Molecular weight:	407.522 g/mol
DrugBank ID:	-
Buried Surface Area:	78.76 %
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:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
3.0511	18.1195	31.502

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
CAB	CG2	VAL- 265	4.25	0	Hydrophobic	false
CAQ	CG2	ILE- 268	4.17	0	Hydrophobic	false
CAB	CD1	ILE- 268	4.02	0	Hydrophobic	false
CAS	CD1	ILE- 268	4.23	0	Hydrophobic	false
CAE	CD1	ILE- 268	4.21	0	Hydrophobic	false
CAX	CG2	ILE- 268	3.49	0	Hydrophobic	false
CAM	CG2	ILE- 268	3.49	0	Hydrophobic	false
CAP	SG	CYS- 269	3.88	0	Hydrophobic	false
CAA	CB	ALA- 272	3.99	0	Hydrophobic	false
CAV	CB	ALA- 272	4.01	0	Hydrophobic	false
CAK	CB	ALA- 272	3.83	0	Hydrophobic	false
CAA	CH2	TRP- 305	4.09	0	Hydrophobic	false
OAH	OD1	ASN- 306	2.66	172.83	H-Bond (Ligand Donor)	false
CAK	CB	LEU- 309	3.61	0	Hydrophobic	false
CAW	CG1	ILE- 310	4.04	0	Hydrophobic	false
CAD	CZ	PHE- 313	4.48	0	Hydrophobic	false
CAE	CZ	PHE- 313	4.19	0	Hydrophobic	false
CAM	CE2	PHE- 313	3.45	0	Hydrophobic	false
OAG	NH2	ARG- 316	3.08	148.88	H-Bond (Protein Donor)	false
OAG	NH1	ARG- 316	3.09	148.14	H-Bond (Protein Donor)	false
OAG	CZ	ARG- 316	3.53	0	Ionic (Protein Cationic)	false
CAE	CD1	ILE- 324	3.6	0	Hydrophobic	false
OAF	N	ALA- 327	3	172.09	H-Bond (Protein Donor)	false
CAB	CG2	VAL- 342	3.96	0	Hydrophobic	false
CAR	CB	VAL- 342	4.12	0	Hydrophobic	false
CAD	CG1	ILE- 345	4.49	0	Hydrophobic	false
CAR	CG2	ILE- 345	3.53	0	Hydrophobic	false
CAE	CD1	PHE- 346	3.7	0	Hydrophobic	false
CAD	CG2	VAL- 349	3.47	0	Hydrophobic	false
CAC	SG	CYS- 432	4.31	0	Hydrophobic	false
CAD	SG	CYS- 432	3.81	0	Hydrophobic	false
CAN	CB	CYS- 432	4.15	0	Hydrophobic	false
CAO	SG	CYS- 432	3.96	0	Hydrophobic	false
CAC	CB	HIS- 435	3.67	0	Hydrophobic	false
CAQ	CB	LEU- 436	4.47	0	Hydrophobic	false
CAA	CD2	LEU- 436	3.66	0	Hydrophobic	false
CAB	CZ	PHE- 439	4.25	0	Hydrophobic	false
CAC	CZ	PHE- 439	4.5	0	Hydrophobic	false
CAA	CD1	LEU- 451	3.83	0	Hydrophobic	false
CAP	CD2	LEU- 451	4.04	0	Hydrophobic	false