scPDB - 2j4a entry

Protein Data Bank Entry:

PDB ID : 2j4a

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2006-08-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thyroid hormone receptor beta
ID:	THB_HUMAN
AC:	P10828
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:	26.546
Number of residues:	41
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.660	313.875

% Hydrophobic	% Polar
80.65	19.35
According to VolSite

Ligand :

HET Code:	OEF
Formula:	C18H17Br2O4
Molecular weight:	457.133 g/mol
DrugBank ID:	-
Buried Surface Area:	82.96 %
Polar Surface area:	69.59 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
4.25183	20.9522	32.0303

Binding mode :

What is Poseview ?

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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
C17	CD1	PHE- 269	4.08	0	Hydrophobic	false
C16	CE1	PHE- 269	3.97	0	Hydrophobic	false
C4	CB	PHE- 272	4.4	0	Hydrophobic	false
BR1	CB	PHE- 272	4.11	0	Hydrophobic	false
C16	CB	PHE- 272	3.95	0	Hydrophobic	false
C17	CB	PHE- 272	4.03	0	Hydrophobic	false
C16	CG2	THR- 273	3.65	0	Hydrophobic	false
BR1	CG1	ILE- 275	3.66	0	Hydrophobic	false
C5	CG1	ILE- 276	4.32	0	Hydrophobic	false
BR1	CB	ILE- 276	3.62	0	Hydrophobic	false
C16	CD1	ILE- 276	4.44	0	Hydrophobic	false
C10	CD1	ILE- 276	3.56	0	Hydrophobic	false
C13	CB	ALA- 279	3.62	0	Hydrophobic	false
O3	NH1	ARG- 282	3.04	139.65	H-Bond (Protein Donor)	false
O4	NH1	ARG- 282	3.48	165.8	H-Bond (Protein Donor)	false
O3	CZ	ARG- 282	3.72	0	Ionic (Protein Cationic)	false
BR2	CE	MET- 310	4.16	0	Hydrophobic	false
C10	SD	MET- 310	3.66	0	Hydrophobic	false
C11	CB	MET- 313	3.87	0	Hydrophobic	false
C14	CB	ARG- 316	4.22	0	Hydrophobic	false
C11	CB	ALA- 317	4.1	0	Hydrophobic	false
C14	CB	ALA- 317	4.23	0	Hydrophobic	false
BR2	CB	ALA- 317	4.44	0	Hydrophobic	false
O4	CZ	ARG- 320	3.63	0	Ionic (Protein Cationic)	false
O4	NH1	ARG- 320	2.8	174.73	H-Bond (Protein Donor)	false
BR1	CD1	LEU- 330	3.99	0	Hydrophobic	false
C5	CD1	LEU- 330	3.66	0	Hydrophobic	false
C11	CD2	LEU- 330	3.77	0	Hydrophobic	false
O4	N	SER- 331	2.79	127.96	H-Bond (Protein Donor)	false
C4	CD1	LEU- 341	4.3	0	Hydrophobic	false
C2	CD1	LEU- 346	4.06	0	Hydrophobic	false
BR2	CD1	LEU- 346	4.38	0	Hydrophobic	false
C15	CD2	LEU- 346	4.28	0	Hydrophobic	false
C8	CD2	LEU- 346	3.72	0	Hydrophobic	false
BR2	CD1	ILE- 353	3.6	0	Hydrophobic	false
O1	NE2	HIS- 435	2.67	165.13	H-Bond (Protein Donor)	false
C8	CE	MET- 442	4.3	0	Hydrophobic	false
C15	SD	MET- 442	3.82	0	Hydrophobic	false
C16	CZ	PHE- 455	3.62	0	Hydrophobic	false
O3	O	HOH- 2024	2.86	179.97	H-Bond (Protein Donor)	false