scPDB - 1nax entry

Protein Data Bank Entry:

PDB ID : 1nax

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2002-11-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	9.430	9.490	9.430	0.090	9.620	3

List of CHEMBLId :

CHEMBL41036

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:	29.502
Number of residues:	41
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.683	324.000

% Hydrophobic	% Polar
77.08	22.92
According to VolSite

Ligand :

HET Code:	IH5
Formula:	C17H15Cl2O4
Molecular weight:	354.205 g/mol
DrugBank ID:	DB03176
Buried Surface Area:	76.8 %
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:	5

Mass center Coordinates

X	Y	Z
4.11774	20.9283	31.9985

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
C16	CE1	PHE- 269	4.02	0	Hydrophobic	false
C18	CD1	PHE- 269	4.35	0	Hydrophobic	false
C4	CB	PHE- 272	4.37	0	Hydrophobic	false
C18	CD1	PHE- 272	3.75	0	Hydrophobic	false
C16	CB	PHE- 272	3.75	0	Hydrophobic	false
C16	CG2	THR- 273	4	0	Hydrophobic	false
CL5	CG1	ILE- 275	3.62	0	Hydrophobic	false
C16	CD1	ILE- 276	4.17	0	Hydrophobic	false
CL5	CB	ILE- 276	4.22	0	Hydrophobic	false
C10	CD1	ILE- 276	3.53	0	Hydrophobic	false
C03	CB	ALA- 279	3.7	0	Hydrophobic	false
C13	CB	ALA- 279	4.18	0	Hydrophobic	false
O4	NH2	ARG- 282	3.24	151.56	H-Bond (Protein Donor)	false
O4	NH1	ARG- 282	3.27	149.71	H-Bond (Protein Donor)	false
O4	CZ	ARG- 282	3.71	0	Ionic (Protein Cationic)	false
CL6	CE	MET- 310	4.05	0	Hydrophobic	false
C10	SD	MET- 310	3.71	0	Hydrophobic	false
C11	CB	MET- 313	3.73	0	Hydrophobic	false
C13	CB	ARG- 316	4.46	0	Hydrophobic	false
CL6	CB	ALA- 317	4.32	0	Hydrophobic	false
C11	CB	ALA- 317	3.91	0	Hydrophobic	false
C03	CB	LEU- 330	4.11	0	Hydrophobic	false
CL5	CD1	LEU- 330	3.89	0	Hydrophobic	false
C07	CD1	LEU- 330	3.69	0	Hydrophobic	false
C09	CD2	LEU- 330	3.67	0	Hydrophobic	false
O3	N	ASN- 331	2.77	143.56	H-Bond (Protein Donor)	false
C4	CD1	LEU- 341	4.1	0	Hydrophobic	false
C18	CG	LEU- 346	4.21	0	Hydrophobic	false
CL6	CD1	LEU- 346	4.33	0	Hydrophobic	false
C2	CD1	LEU- 346	3.99	0	Hydrophobic	false
C8	CD2	LEU- 346	3.68	0	Hydrophobic	false
CL6	CD1	ILE- 353	3.69	0	Hydrophobic	false
O1	NE2	HIS- 435	2.82	158.25	H-Bond (Protein Donor)	false
C8	CE	MET- 442	4.36	0	Hydrophobic	false
C14	SD	MET- 442	4.05	0	Hydrophobic	false
C16	CZ	PHE- 455	3.96	0	Hydrophobic	false
O3	O	HOH- 606	2.73	154.57	H-Bond (Protein Donor)	false
O4	O	HOH- 607	3.05	150.28	H-Bond (Protein Donor)	false