scPDB - 2lbd entry

Protein Data Bank Entry:

PDB ID : 2lbd

Resolution :2.060 Å

Experimental Method : X-ray

Deposition Date : 1997-08-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.720	8.290	7.780	0.720	9.700	18

List of CHEMBLId :

CHEMBL38

Binding Site :

Uniprot Annotation

Name:	Retinoic acid receptor gamma
ID:	RARG_HUMAN
AC:	P13631
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:	19.056
Number of residues:	39
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.863	465.750

% Hydrophobic	% Polar
77.54	22.46
According to VolSite

Ligand :

HET Code:	REA
Formula:	C20H27O2
Molecular weight:	299.427 g/mol
DrugBank ID:	DB00755
Buried Surface Area:	79.54 %
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
40.4326	15.5099	84.1661

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	CE1	PHE- 201	4.39	0	Hydrophobic	false
C4	CZ3	TRP- 227	4.4	0	Hydrophobic	false
C17	CE2	PHE- 230	3.88	0	Hydrophobic	false
C18	CB	ALA- 234	4.47	0	Hydrophobic	false
C20	SG	CYS- 237	3.84	0	Hydrophobic	false
C19	CD2	LEU- 268	4.46	0	Hydrophobic	false
C19	CB	LEU- 271	3.78	0	Hydrophobic	false
C16	CE	MET- 272	3.69	0	Hydrophobic	false
C19	SD	MET- 272	3.74	0	Hydrophobic	false
C20	CB	ARG- 274	3.7	0	Hydrophobic	false
C19	CG1	ILE- 275	3.82	0	Hydrophobic	false
C20	CG2	ILE- 275	3.52	0	Hydrophobic	false
O2	NH1	ARG- 278	3.17	149.69	H-Bond (Protein Donor)	false
O1	OG	SER- 289	3.21	139.83	H-Bond (Protein Donor)	false
O1	N	SER- 289	2.71	178.06	H-Bond (Protein Donor)	false
O2	OG	SER- 289	2.92	153.07	H-Bond (Protein Donor)	false
O2	N	SER- 289	3.45	127.5	H-Bond (Protein Donor)	false
C16	CE2	PHE- 304	3.86	0	Hydrophobic	false
C17	CD2	PHE- 304	3.99	0	Hydrophobic	false
C19	CZ	PHE- 304	4.21	0	Hydrophobic	false
C16	CD2	LEU- 307	4.4	0	Hydrophobic	false
C2	CG	ARG- 396	4.13	0	Hydrophobic	false
C3	CB	ALA- 397	4.07	0	Hydrophobic	false
C17	CD1	LEU- 400	4.43	0	Hydrophobic	false
C3	CD1	LEU- 400	3.44	0	Hydrophobic	false
C3	CE	MET- 408	4.33	0	Hydrophobic	false
C18	CG2	ILE- 412	4.14	0	Hydrophobic	false
C18	CE	MET- 415	4.1	0	Hydrophobic	false