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RORB_RAT_214_465_ligBind

Nuclear receptor ROR-beta [Nuclear hormone receptor family. NR1 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (RORB_RAT):D: NR LBD (238:240, 273, 276, 277, 280, 311, 314, 315, 317, 318, 320, 321, 329:331, 341, 344, 349, 350, 353, 354, 430, 434)238:240, 273, 276, 277, 280, 311, 314, 315, 317, 318, 320, 321, 329:331, 341, 344, 349, 350, 353, 354, 430, 434

Full PDB list

1k4w, 1n4h, 1nq7

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
C
2
3
8
Q
2
3
9
Y
2
4
0
C
2
7
3
Q
2
7
6
I
2
7
7
A
2
8
0
L
3
1
1
V
3
1
4
L
3
1
5
R
3
1
7
M
3
1
8
A
3
2
1
V
3
2
9
L
3
3
0
F
3
3
1
F
3
4
1
L
3
4
9
V
3
5
0
A
3
5
3
F
3
5
4
V
4
3
0
H
4
3
4
[1]1k4w.a ste20 . . . . . . . . . . . . . . . . . . . . . . .
[1]1n4h.a rea22 . . . . . . . . . . . . . . . . . . . . . . .
[1]1nq7.a arl25 . . . . . . . . . . . . . . . . . . . . . . .

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
C
2
3
8
Q
2
3
9
Y
2
4
0
C
2
7
3
Q
2
7
6
I
2
7
7
A
2
8
0
L
3
1
1
V
3
1
4
L
3
1
5
R
3
1
7
M
3
1
8
R
3
2
0
A
3
2
1
V
3
2
9
L
3
3
0
F
3
3
1
F
3
4
1
L
3
4
4
L
3
4
9
V
3
5
0
A
3
5
3
F
3
5
4
V
4
3
0
H
4
3
4
[1]1k4w.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1n4h.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1nq7.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
1k4w.a:ste
1n4h.a:rea
1nq7.a:arl
[1] 1k4w.a
0
0 0
[1] 1n4h.a 0.3
0
0.3
[1] 1nq7.a 0 0
0
[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
1k4w.a
1n4h.a
1nq7.a
[1] 1k4w.a
0
.02 0
[1] 1n4h.a .02
0
.02
[1] 1nq7.a 0 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone 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
1k4w.a
1n4h.a
1nq7.a
[1] 1k4w.a
0
0.4 0.5
[1] 1n4h.a 0.4
0
0.3
[1] 1nq7.a 0.5 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
1k4w.a
1n4h.a
1nq7.a
[1] 1k4w.a
0
0.5 0.7
[1] 1n4h.a 0.5
0
0.6
[1] 1nq7.a 0.7 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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