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THA_HUMAN_148_375

Thyroid hormone receptor alpha [Nuclear hormone receptor family. NR1 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (THA_HUMAN):D: NR LBD (215, 218, 219, 221, 222, 225, 228, 256, 259, 260, 262, 263, 266, 275:278, 287, 290:292, 299, 381, 388, 401)215, 218, 219, 221, 222, 225, 228, 256, 259, 260, 262, 263, 266, 275:278, 287, 290:292, 299, 381, 388, 401

Full PDB list

1nav, 2h77, 2h79, 3hzf, 3ilz, 3jzb, 4lnw, 4lnx (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
2
1
5
F
2
1
8
T
2
1
9
I
2
2
1
I
2
2
2
A
2
2
5
R
2
2
8
M
2
5
6
M
2
5
9
S
2
6
0
R
2
6
2
A
2
6
3
R
2
6
6
L
2
7
6
S
2
7
7
G
2
7
8
L
2
8
7
G
2
9
0
G
2
9
1
L
2
9
2
I
2
9
9
H
3
8
1
M
3
8
8
F
4
0
1
[1]1nav.a ih523 . . . . . . . . . . . . . . . . . . . . . . . .
[1]2h79.a t323 . . . . . . . . . . . . . . . . . . . . . . * .
[1]3ilz.a b7224 . . . . . . . . . . . . . . . . . . . . . . . .
[1]3jzb.a 4hy21 . . . . . . . . . . . . . . . . . . . . . . . .
[1]4lnw.a t323 . . . . . . . . . . . . . . . . . . . . . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

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PDB.ch
A1
F
2
1
5
F
2
1
8
T
2
1
9
I
2
2
1
I
2
2
2
A
2
2
5
R
2
2
8
M
2
5
6
M
2
5
9
S
2
6
0
R
2
6
2
A
2
6
3
R
2
6
6
T
2
7
5
L
2
7
6
S
2
7
7
G
2
7
8
L
2
8
7
G
2
9
0
G
2
9
1
L
2
9
2
I
2
9
9
H
3
8
1
M
3
8
8
F
4
0
1
[1]1nav.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2h79.a . . . . . . . . . . . . . . . . . . . . . . . * .
[1]3ilz.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3jzb.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4lnw.a . . . . . . . . . . . . . . . . . . . . . . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1nav.a:ih5
2h79.a:t3
3ilz.a:b72
3jzb.a:4hy
4lnw.a:t3
[1] 1nav.a
0.1
0.2 0.1 0.2 0.1
[1] 2h79.a 0.3
0.2
0.2 0.1 0.1
[1] 3ilz.a 0.1 0
0
0.1 0
[1] 3jzb.a 0.5 0.7 0.3
0.2
0.7
[1] 4lnw.a 0.2 0.1 0.1 0.1
0.1
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1nav.a
2h79.a
3ilz.a
3jzb.a
4lnw.a
[1] 1nav.a
0
.02 .02 .04 .01
[1] 2h79.a .02
0
.01 .03 0
[1] 3ilz.a .02 .01
0
.04 .01
[1] 3jzb.a .04 .03 .04
0
.03
[1] 4lnw.a .01 0 .01 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1nav.a
2h79.a
3ilz.a
3jzb.a
4lnw.a
[1] 1nav.a
0
0.5 0.6 0.5 0.5
[1] 2h79.a 0.5
0
0.5 0.2 0.1
[1] 3ilz.a 0.6 0.5
0
0.6 0.5
[1] 3jzb.a 0.5 0.2 0.6
0
0.2
[1] 4lnw.a 0.5 0.1 0.5 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1nav.a
2h79.a
3ilz.a
3jzb.a
4lnw.a
[1] 1nav.a
0
0.8 0.8 0.9 0.8
[1] 2h79.a 0.8
0
0.7 0.6 0.5
[1] 3ilz.a 0.8 0.7
0
0.7 0.7
[1] 3jzb.a 0.9 0.6 0.7
0
0.7
[1] 4lnw.a 0.8 0.5 0.7 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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