scPDB - 3d57 entry

Protein Data Bank Entry:

PDB ID : 3d57

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2008-05-15

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:	20.826
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.612	411.750

% Hydrophobic	% Polar
71.31	28.69
According to VolSite

Ligand :

HET Code:	4HY
Formula:	C14H8I3O4
Molecular weight:	620.924 g/mol
DrugBank ID:	DB03604
Buried Surface Area:	75.52 %
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:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
45.8101	-0.50245	37.94

Binding mode :

What is Poseview ?

2D View
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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
I2	CD1	PHE- 269	3.89	0	Hydrophobic	false
C4	CB	PHE- 272	4.11	0	Hydrophobic	false
I1	CB	PHE- 272	4.44	0	Hydrophobic	false
I2	CB	PHE- 272	4.02	0	Hydrophobic	false
I1	CG1	ILE- 275	3.9	0	Hydrophobic	false
I1	CB	ILE- 276	4.06	0	Hydrophobic	false
C10	CD1	ILE- 276	3.72	0	Hydrophobic	false
C3	CB	ALA- 279	3.87	0	Hydrophobic	false
C10	CE	MET- 310	3.94	0	Hydrophobic	false
C12	SD	MET- 310	4.08	0	Hydrophobic	false
C12	CE	MET- 313	4.32	0	Hydrophobic	false
C11	CB	MET- 313	3.83	0	Hydrophobic	false
I3	CB	ALA- 317	4.08	0	Hydrophobic	false
C11	CB	ALA- 317	3.73	0	Hydrophobic	false
O3	NH1	ARG- 320	3.05	153.64	H-Bond (Protein Donor)	false
O4	NH2	ARG- 320	2.94	158.38	H-Bond (Protein Donor)	false
O4	NH1	ARG- 320	3.37	136.27	H-Bond (Protein Donor)	false
O4	CZ	ARG- 320	3.6	0	Ionic (Protein Cationic)	false
C3	CB	LEU- 330	4.27	0	Hydrophobic	false
I1	CD1	LEU- 330	4.31	0	Hydrophobic	false
I3	CD2	LEU- 330	4.36	0	Hydrophobic	false
C7	CD1	LEU- 330	3.98	0	Hydrophobic	false
C9	CD2	LEU- 330	3.83	0	Hydrophobic	false
O3	N	ASN- 331	2.86	168.31	H-Bond (Protein Donor)	false
O4	N	ASN- 331	3.34	133.12	H-Bond (Protein Donor)	false
C4	CD1	LEU- 341	4.49	0	Hydrophobic	false
I2	CD2	LEU- 346	4.33	0	Hydrophobic	false
I3	CD1	LEU- 346	4.21	0	Hydrophobic	false
C4	CD1	LEU- 346	4.18	0	Hydrophobic	false
C8	CD2	LEU- 346	3.52	0	Hydrophobic	false
I3	CD1	ILE- 353	3.66	0	Hydrophobic	false
O1	NE2	HIS- 435	2.74	157.82	H-Bond (Protein Donor)	false