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THB_HUMAN_205_461_ligBind

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (THB_HUMAN):D: NR LBD (269, 272, 273, 275, 276, 279, 282, 310, 313, 314, 316, 317, 320, 329:331, 341, 344:346, 353, 435, 438, 439, 442, 451, 455, 459)
R: Interaction with NR2F6 (269, 272, 273, 275, 276, 279, 282, 310, 313, 314, 316, 317, 320, 329:331, 341, 344:346, 353, 435, 438, 439, 442, 451, 455, 459)
269, 272, 273, 275, 276, 279, 282, 310, 313, 314, 316, 317, 320, 329:331, 341, 344:346, 353, 435, 438, 439, 442, 451, 455, 459

Full PDB list

1n46, 1nax, 1nq0, 1nq1, 1nq2, 1nuo, 1q4x, 1r6g, 1xzx, 1y0x, 2j4a, 2pin, 3d57, 3gws, 3imy, 3jzc, 4zo1 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
2
6
9
F
2
7
2
T
2
7
3
I
2
7
5
I
2
7
6
A
2
7
9
R
2
8
2
M
3
1
0
M
3
1
3
S
3
1
4
R
3
1
6
A
3
1
7
R
3
2
0
L
3
3
0
N
3
3
1
L
3
4
1
G
3
4
4
G
3
4
5
L
3
4
6
I
3
5
3
H
4
3
5
R
4
3
8
F
4
3
9
M
4
4
2
F
4
5
1
F
4
5
5
F
4
5
9
[1]1n46.a pfa27 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1nax.a ih523 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1nq2.a 4hy21 . . . . . . . . . . . T . . . . . . . . . . . . . . .
[1]1nuo.a 4hy21 . . . . . . . . . . H . . . . . . . . . . . . . . . .
[1]1q4x.a g2428 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1r6g.a 44231 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1y0x.x t4424 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2j4a.a oef24 . . . . . . . . . . . . . . S . . . . . . . . . . . .
[1]3d57.a 4hy21 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3imy.a b7224 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4zo1.x 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

[download in TSV format]
   
PDB.ch
A1
F
2
6
9
F
2
7
2
T
2
7
3
I
2
7
5
I
2
7
6
A
2
7
9
R
2
8
2
M
3
1
0
M
3
1
3
S
3
1
4
R
3
1
6
A
3
1
7
R
3
2
0
T
3
2
9
L
3
3
0
N
3
3
1
L
3
4
1
G
3
4
4
G
3
4
5
L
3
4
6
I
3
5
3
H
4
3
5
R
4
3
8
F
4
3
9
M
4
4
2
F
4
5
1
F
4
5
5
F
4
5
9
[1]1n46.a . . * . . . . . . . . . . . . . . . . . . . . . * . . .
[1]1nax.a . . . . . . . . . . . . . . . . . . . . . . . . * . . .
[1]1nq2.a . . * . . . . . . . . T . . . . . . . . . . . . * . . .
[1]1nuo.a . . . . . . . . . . H . . . . . . . . . . . . . * . . .
[1]1q4x.a . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1r6g.a . . * . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1y0x.x . . * . . . . . . . . . . . . . . . . . . . . . * . . .
[1]2j4a.a . . * . . . . . . . . . . . . S . . . . . . . . * . . .
[1]3d57.a . . * . . . . . . . . . . . . . . . . . . . . . * . . .
[1]3imy.a . . . . . . . . . . . . . . . . . . . . . . . . * . . .
[1]4zo1.x . . * . . . . . . . . . . . . . . . . . . . . . * . . .

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
1n46.a:pfa
1nax.a:ih5
1nq2.a:4hy
1nuo.a:4hy
1q4x.a:g24
1r6g.a:442
1y0x.x:t44
2j4a.a:oef
3d57.a:4hy
3imy.a:b72
4zo1.x:t3
[1] 1n46.a
0.1
0.3 0.2 0.5 1.8 2.3 1.1 0.5 0.3 0.3 0.6
[1] 1nax.a 0.1
0
0.1 0.1 1.3 1.9 0.4 0 0.1 0 0.1
[1] 1nq2.a 0.3 0.3
0.1
0.3 1.5 1.8 0.2 0.2 0.2 0.3 0.1
[1] 1nuo.a 0.5 0.3 0.7
0.5
1.1 2.9 1.0 0.6 0.6 0.4 1.1
[1] 1q4x.a 0.1 0 0 0.1
0
0.2 0.1 0 0.1 0 0.1
[1] 1r6g.a 0.5 0.2 0.1 0.1 1.4
0
0.8 0.4 0.2 0.4 0.6
[1] 1y0x.x 0.4 0.1 0.1 0.2 1.4 1.9
0.2
0.1 0.1 0.1 0.2
[1] 2j4a.a 0.3 0.2 0.4 0.2 1.8 2.4 0.7
0
0.2 0.1 0.5
[1] 3d57.a 0.2 0.2 0.1 0.4 1.9 2.2 0.6 0.2
0
0.2 0.4
[1] 3imy.a 0.2 0 0.1 0.1 0.5 1.6 0.3 0.1 0.2
0.1
0
[1] 4zo1.x 0.1 0.1 0 0 1.1 1.5 0.4 0.2 0 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
1n46.a
1nax.a
1nq2.a
1nuo.a
1q4x.a
1r6g.a
1y0x.x
2j4a.a
3d57.a
3imy.a
4zo1.x
[1] 1n46.a
0
.07 .10 .08 .18 .18 .08 .10 .07 .11 .12
[1] 1nax.a .07
0
.08 .10 .13 .15 .04 .06 .07 .05 .09
[1] 1nq2.a .10 .08
0
.11 .13 .11 .07 .09 .08 .08 .05
[1] 1nuo.a .08 .10 .11
0
.16 .17 .11 .12 .11 .09 .12
[1] 1q4x.a .18 .13 .13 .16
0
.09 .14 .17 .18 .09 .13
[1] 1r6g.a .18 .15 .11 .17 .09
0
.14 .15 .16 .12 .10
[1] 1y0x.x .08 .04 .07 .11 .14 .14
0
.05 .06 .07 .09
[1] 2j4a.a .10 .06 .09 .12 .17 .15 .05
0
.05 .10 .10
[1] 3d57.a .07 .07 .08 .11 .18 .16 .06 .05
0
.10 .09
[1] 3imy.a .11 .05 .08 .09 .09 .12 .07 .10 .10
0
.06
[1] 4zo1.x .12 .09 .05 .12 .13 .10 .09 .10 .09 .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
1n46.a
1nax.a
1nq2.a
1nuo.a
1q4x.a
1r6g.a
1y0x.x
2j4a.a
3d57.a
3imy.a
4zo1.x
[1] 1n46.a
0
0.4 0.5 0.6 1.1 0.8 0.4 0.5 0.3 0.5 0.5
[1] 1nax.a 0.4
0
0.5 0.6 1.0 0.7 0.4 0.4 0.4 0.4 0.5
[1] 1nq2.a 0.5 0.5
0
0.6 1.0 0.5 0.3 0.5 0.5 0.4 0.4
[1] 1nuo.a 0.6 0.6 0.6
0
1.1 0.8 0.5 0.7 0.6 0.6 0.7
[1] 1q4x.a 1.1 1.0 1.0 1.1
0
0.9 0.9 1.1 1.1 0.9 1.0
[1] 1r6g.a 0.8 0.7 0.5 0.8 0.9
0
0.6 0.7 0.7 0.5 0.6
[1] 1y0x.x 0.4 0.4 0.3 0.5 0.9 0.6
0
0.4 0.4 0.3 0.4
[1] 2j4a.a 0.5 0.4 0.5 0.7 1.1 0.7 0.4
0
0.4 0.5 0.5
[1] 3d57.a 0.3 0.4 0.5 0.6 1.1 0.7 0.4 0.4
0
0.5 0.5
[1] 3imy.a 0.5 0.4 0.4 0.6 0.9 0.5 0.3 0.5 0.5
0
0.4
[1] 4zo1.x 0.5 0.5 0.4 0.7 1.0 0.6 0.4 0.5 0.5 0.4
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

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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
1n46.a
1nax.a
1nq2.a
1nuo.a
1q4x.a
1r6g.a
1y0x.x
2j4a.a
3d57.a
3imy.a
4zo1.x
[1] 1n46.a
0
0.8 1.0 0.9 1.4 1.2 0.9 0.8 0.7 1.0 0.9
[1] 1nax.a 0.8
0
0.9 0.7 1.1 1.0 0.6 0.5 0.7 0.8 0.7
[1] 1nq2.a 1.0 0.9
0
0.9 1.2 1.1 0.7 0.9 0.9 0.8 0.7
[1] 1nuo.a 0.9 0.7 0.9
0
1.2 1.1 0.7 0.8 0.8 0.8 0.8
[1] 1q4x.a 1.4 1.1 1.2 1.2
0
1.0 1.1 1.2 1.3 1.1 1.1
[1] 1r6g.a 1.2 1.0 1.1 1.1 1.0
0
1.0 1.0 1.1 1.0 0.9
[1] 1y0x.x 0.9 0.6 0.7 0.7 1.1 1.0
0
0.6 0.8 0.7 0.5
[1] 2j4a.a 0.8 0.5 0.9 0.8 1.2 1.0 0.6
0
0.6 0.8 0.7
[1] 3d57.a 0.7 0.7 0.9 0.8 1.3 1.1 0.8 0.6
0
1.0 0.8
[1] 3imy.a 1.0 0.8 0.8 0.8 1.1 1.0 0.7 0.8 1.0
0
0.7
[1] 4zo1.x 0.9 0.7 0.7 0.8 1.1 0.9 0.5 0.7 0.8 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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