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RARA_HUMAN_173_420

Retinoic acid receptor alpha [Nuclear hormone receptor family. NR1 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (RARA_HUMAN):D: NR LBD (199, 225, 228, 229, 231:233, 235, 236, 266, 269, 270, 272, 273, 276, 286, 287, 301, 302, 305, 309, 391, 394:396, 398, 399, 406:410, 414, 415)199, 225, 228, 229, 231:233, 235, 236, 266, 269, 270, 272, 273, 276, 286, 287, 301, 302, 305, 309, 391, 394:396, 398, 399, 406:410, 414, 415

Full PDB list

1dkf, 3a9e, 3kmr, 3kmz, 4dqm, 5k13

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
1
9
9
W
2
2
5
F
2
2
8
S
2
2
9
L
2
3
1
S
2
3
2
T
2
3
3
C
2
3
5
I
2
3
6
L
2
6
6
L
2
6
9
I
2
7
0
R
2
7
2
I
2
7
3
R
2
7
6
F
2
8
6
S
2
8
7
G
3
0
1
F
3
0
2
L
3
0
5
G
3
9
1
R
3
9
4
V
3
9
5
L
3
9
8
M
4
0
6
P
4
0
7
I
4
1
0
L
4
1
4
[1]1dkf.b bms34 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3a9e.b rea22 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3kmr.a eqn26 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3kmz.b eqo,L39 . . . . . . . . . . . . . . . . . . . . . . . . - - - -
[1]4dqm.a luf28 . . . . . . . * . . . . . . . . . . . . . . . . . . . .
[1]5k13.a 6q734 . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
1
9
9
W
2
2
5
F
2
2
8
S
2
2
9
L
2
3
1
S
2
3
2
T
2
3
3
C
2
3
5
I
2
3
6
L
2
6
6
L
2
6
9
I
2
7
0
R
2
7
2
I
2
7
3
R
2
7
6
F
2
8
6
S
2
8
7
G
3
0
1
F
3
0
2
L
3
0
5
V
3
0
9
G
3
9
1
R
3
9
4
V
3
9
5
I
3
9
6
L
3
9
8
K
3
9
9
M
4
0
6
P
4
0
7
P
4
0
8
L
4
0
9
I
4
1
0
L
4
1
4
E
4
1
5
[1]1dkf.b . . . . . . . . . . . . . . . . * . . . . . . * . . . * . . . . . .
[1]3a9e.b . . . . . . . . . . . . . . . . * . . . . . . * . . . . . . . * * .
[1]3kmr.a . . . . . . . . . . . . . . . . * . . . . . . * . . . . . . . * * .
[1]3kmz.b . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - - -
[1]4dqm.a . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . * * .
[1]5k13.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
1dkf.b:bms
3a9e.b:rea
3kmr.a:eqn
3kmz.b:L,eqo
4dqm.a:luf
5k13.a:6q7
[1] 1dkf.b
0
0 0.2 2.0 2.9 1.9
[1] 3a9e.b 1.9
0
0 4.3 2.7 0.9
[1] 3kmr.a 2.3 0.2
0
5.8 2.6 1.4
[1] 3kmz.b 0 0 0.1
0
1.7 1.5
[1] 4dqm.a 2.8 0.3 0.5 4.3
1.8
1.3
[1] 5k13.a 0.8 0 0.1 2.3 3.0
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
1dkf.b
3a9e.b
3kmr.a
3kmz.b
4dqm.a
5k13.a
[1] 1dkf.b
0
.17 .20 .15 .24 .10
[1] 3a9e.b .17
0
.08 .21 .10 .14
[1] 3kmr.a .20 .08
0
.24 .11 .17
[1] 3kmz.b .15 .21 .24
0
.23 .14
[1] 4dqm.a .24 .10 .11 .23
0
.21
[1] 5k13.a .10 .14 .17 .14 .21
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.8 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
1dkf.b
3a9e.b
3kmr.a
3kmz.b
4dqm.a
5k13.a
[1] 1dkf.b
0
4.4 4.4 2.7 4.4 2.6
[1] 3a9e.b 4.4
0
0.4 2.8 0.8 2.7
[1] 3kmr.a 4.4 0.4
0
2.9 0.7 2.7
[1] 3kmz.b 2.7 2.8 2.9
0
2.8 2.9
[1] 4dqm.a 4.4 0.8 0.7 2.8
0
2.7
[1] 5k13.a 2.6 2.7 2.7 2.9 2.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 2.7 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
1dkf.b
3a9e.b
3kmr.a
3kmz.b
4dqm.a
5k13.a
[1] 1dkf.b
0
4.5 4.5 3.4 4.5 2.8
[1] 3a9e.b 4.5
0
0.7 3.5 0.9 2.8
[1] 3kmr.a 4.5 0.7
0
3.6 0.9 2.8
[1] 3kmz.b 3.4 3.5 3.6
0
3.4 3.6
[1] 4dqm.a 4.5 0.9 0.9 3.4
0
2.9
[1] 5k13.a 2.8 2.8 2.8 3.6 2.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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