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RXRB_HUMAN_289_527_ligBind

Retinoic acid receptor RXR-beta [Nuclear hormone receptor family. NR2 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (RXRB_HUMAN):D: NR LBD (336, 339, 340, 342, 343, 346, 376, 377, 380, 381, 384, 387, 397, 398, 413, 416, 420, 503, 506, 507, 510)336, 339, 340, 342, 343, 346, 376, 377, 380, 381, 384, 387, 397, 398, 413, 416, 420, 503, 506, 507, 510

Full PDB list

1h9u, 1uhl, 5hjp, 5i4v, 5kya, 5kyj (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
3
3
9
A
3
4
2
A
3
4
3
Q
3
4
6
W
3
7
6
L
3
8
0
I
3
8
1
F
3
8
4
R
3
8
7
L
3
9
7
A
3
9
8
V
4
1
3
I
4
1
6
V
4
2
0
C
5
0
3
H
5
0
6
L
5
0
7
[1]1h9u.a lg227 . . . . . . . . . . . . . . . . .
[1]1uhl.a mei19 . . . . . . . . . . . . . . . . .
[1]5hjp.c none . . . . . . . . . . . . . . . . .

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
V
3
3
6
I
3
3
9
C
3
4
0
A
3
4
2
A
3
4
3
Q
3
4
6
W
3
7
6
N
3
7
7
L
3
8
0
I
3
8
1
F
3
8
4
R
3
8
7
L
3
9
7
A
3
9
8
V
4
1
3
I
4
1
6
V
4
2
0
C
5
0
3
H
5
0
6
L
5
0
7
F
5
1
0
[1]1h9u.a . . . . . . . . . . . . . . . . . . . . .
[1]1uhl.a . . . . . . . . . . . . . . . . . . . . .
[1]5hjp.c . . . . . . . . . . . . . . . . . . . . .

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
1h9u.a:lg2
1uhl.a:mei
5hjp.c is apo
[1] 1h9u.a
0
0.4 -
[1] 1uhl.a 0.5
0
-
[1] 5hjp.c 0.9 0.3
-
[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
1h9u.a
1uhl.a
5hjp.c
[1] 1h9u.a
0
.03 .05
[1] 1uhl.a .03
0
.03
[1] 5hjp.c .05 .03
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
1h9u.a
1uhl.a
5hjp.c
[1] 1h9u.a
0
0.6 0.5
[1] 1uhl.a 0.6
0
0.4
[1] 5hjp.c 0.5 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
1h9u.a
1uhl.a
5hjp.c
[1] 1h9u.a
0
1.0 1.0
[1] 1uhl.a 1.0
0
0.8
[1] 5hjp.c 1.0 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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