scPDB - 1fby entry

Protein Data Bank Entry:

PDB ID : 1fby

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2000-07-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	5.740	7.630	7.970	0.900	8.820	14

List of CHEMBLId :

CHEMBL705

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
B	100 %

Ligand binding site composition:

B-Factor:	45.762
Number of residues:	39
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
2.149	472.500

% Hydrophobic	% Polar
83.57	16.43
According to VolSite

Ligand :

HET Code:	REA
Formula:	C20H27O2
Molecular weight:	299.427 g/mol
DrugBank ID:	DB00755
Buried Surface Area:	65.86 %
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
31.8095	41.6154	24.6363

Binding mode :

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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
C20	CG2	ILE- 1268	3.82	0	Hydrophobic	false
C16	CG2	ILE- 1268	4.04	0	Hydrophobic	false
C4	CD1	ILE- 1268	4.01	0	Hydrophobic	false
C16	SG	CYS- 1269	3.98	0	Hydrophobic	false
C20	CB	ALA- 1271	3.69	0	Hydrophobic	false
C19	CZ3	TRP- 1305	4.19	0	Hydrophobic	false
C19	CB	ASN- 1306	4.11	0	Hydrophobic	false
C19	CG1	ILE- 1310	4.37	0	Hydrophobic	false
C18	CZ	PHE- 1313	3.65	0	Hydrophobic	false
C20	CD2	PHE- 1313	3.94	0	Hydrophobic	false
O1	NH1	ARG- 1316	3.14	127.3	H-Bond (Protein Donor)	false
O1	NH2	ARG- 1316	2.52	163.36	H-Bond (Protein Donor)	false
O2	NH2	ARG- 1316	2.78	123.32	H-Bond (Protein Donor)	false
O1	CZ	ARG- 1316	3.24	0	Ionic (Protein Cationic)	false
O2	CZ	ARG- 1316	3.99	0	Ionic (Protein Cationic)	false
C20	CD2	LEU- 1326	3.53	0	Hydrophobic	false
O2	N	ALA- 1327	2.62	147.09	H-Bond (Protein Donor)	false
C2	CG1	VAL- 1342	4.4	0	Hydrophobic	false
C3	CG2	VAL- 1342	3.69	0	Hydrophobic	false
C3	CG2	ILE- 1345	3.81	0	Hydrophobic	false
C18	CG2	VAL- 1349	4.09	0	Hydrophobic	false
C17	CB	CYS- 1432	4.39	0	Hydrophobic	false
C18	SG	CYS- 1432	4.03	0	Hydrophobic	false
C19	CB	CYS- 1432	4.24	0	Hydrophobic	false
C17	CB	HIS- 1435	3.5	0	Hydrophobic	false
C16	CD2	LEU- 1436	4.02	0	Hydrophobic	false
C16	CE1	PHE- 1439	4.06	0	Hydrophobic	false
C17	CE1	PHE- 1439	4.05	0	Hydrophobic	false