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NR1H3_HUMAN_189_447_coactiv

Oxysterols receptor LXR-alpha [Nuclear hormone receptor family. NR1 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (NR1H3_HUMAN):R: Transactivation AF-2
required for ligand-dependent transactivation function
mediates interaction with CCAR2 (227, 265, 266, 269, 273, 278, 279, 283, 284, 286, 287, 290, 291, 437, 438, 441, 442, 445)
D: NR LBD (227, 265, 266, 269, 273, 278, 279, 283, 284, 286, 287, 290, 291, 437, 438, 441, 442, 445)
227, 265, 266, 269, 273, 278, 279, 283, 284, 286, 287, 290, 291, 437, 438, 441, 442, 445

Full PDB list

1uhl, 2acl, 3fal, 3fc6, 3ipq, 3ips, 3ipu, 5avi, 5avl, 5hjs (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
V
2
6
5
Q
2
6
6
V
2
6
9
K
2
7
3
F
2
7
8
R
2
8
3
E
2
8
4
Q
2
8
6
I
2
8
7
L
2
9
0
K
2
9
1
P
4
3
7
L
4
3
8
E
4
4
1
I
4
4
2
V
4
4
5
[1]1uhl.b HKILHRLLQD89 . . . . . . . . . . . . . . . .
[1]2acl.b IDTFLMEMLEA89 . . . . . . . . . . . . . . . .
[1]2acl.d PIDTFLMEMLEAP103 . . . . . . . . . . . . . . . .
[1]2acl.f PIDTFLMEMLEA96 . . . . . . . . . . . . . . . .
[1]3fal.b TFLMEMLEA63 . . . . . . . . . . . . . . . .
[1]3fc6.b DTFLMEMLEA81 . . . . . . . . . . . . . . . .
[1]5avl.a TERHKILHRLLQE117 . . . . . . . . . . . . . . . .
[1]5hjs.a RHKILHRLLQE101 . . . . . . . . . . . . . . . .

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
R
2
2
7
V
2
6
5
Q
2
6
6
V
2
6
9
K
2
7
3
F
2
7
8
L
2
7
9
R
2
8
3
E
2
8
4
Q
2
8
6
I
2
8
7
L
2
9
0
K
2
9
1
P
4
3
7
L
4
3
8
E
4
4
1
I
4
4
2
V
4
4
5
[1]1uhl.b . . . . . . . . . . . . . . . * . .
[1]2acl.b . . . . . . . . . . . . * . . . . .
[1]2acl.d . . . . . . . . . . . . * . . . . .
[1]2acl.f . . . . . . . . . . . . * . . . . .
[1]3fal.b . . . . . . . . . . . . . . . . . .
[1]3fc6.b . . . . . . . . . . . . * . . . . .
[1]5avl.a - . . . . . . . . . . . . . . . . .
[1]5hjs.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
1uhl.b:HKILHRLLQD
2acl.b:IDTFLMEMLEA
2acl.d:PIDTFLMEMLEAP
2acl.f:PIDTFLMEMLEA
3fal.b:TFLMEMLEA
3fc6.b:DTFLMEMLEA
5avl.a:TERHKILHRLLQE
5hjs.a:RHKILHRLLQE
[1] 1uhl.b
0.1
2.1 1.1 0.9 0.8 0.9 2.6 1.2
[1] 2acl.b 0.2
0.2
0.7 0.4 0.1 0 1.1 0.8
[1] 2acl.d 0 0.8
0.1
0.2 0.1 0.2 2.2 1.5
[1] 2acl.f 0.3 0.8 0.4
0
0.3 0.4 1.9 1.5
[1] 3fal.b 0.3 0.1 0.5 0.3
0
0.1 1.3 0.9
[1] 3fc6.b 0.1 0.3 0.7 0.2 0
0
1.4 1.4
[1] 5avl.a 0 0.5 0.5 0.3 0.3 0.2
0.1
0
[1] 5hjs.a 0 0.6 0.6 0.4 0.2 0.2 0.5
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
1uhl.b
2acl.b
2acl.d
2acl.f
3fal.b
3fc6.b
5avl.a
5hjs.a
[1] 1uhl.b
0
.12 .18 .17 .13 .15 .16 .16
[1] 2acl.b .12
0
.11 .08 .03 .05 .07 .06
[1] 2acl.d .18 .11
0
.06 .08 .08 .14 .12
[1] 2acl.f .17 .08 .06
0
.06 .08 .13 .11
[1] 3fal.b .13 .03 .08 .06
0
.07 .09 .06
[1] 3fc6.b .15 .05 .08 .08 .07
0
.10 .08
[1] 5avl.a .16 .07 .14 .13 .09 .10
0
.05
[1] 5hjs.a .16 .06 .12 .11 .06 .08 .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 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
1uhl.b
2acl.b
2acl.d
2acl.f
3fal.b
3fc6.b
5avl.a
5hjs.a
[1] 1uhl.b
0
1.5 1.7 1.6 1.2 1.2 1.1 1.0
[1] 2acl.b 1.5
0
0.6 0.8 0.7 0.5 1.2 1.3
[1] 2acl.d 1.7 0.6
0
0.8 0.9 0.8 1.4 1.4
[1] 2acl.f 1.6 0.8 0.8
0
0.7 0.8 1.0 1.2
[1] 3fal.b 1.2 0.7 0.9 0.7
0
0.4 0.9 1.0
[1] 3fc6.b 1.2 0.5 0.8 0.8 0.4
0
1.0 1.0
[1] 5avl.a 1.1 1.2 1.4 1.0 0.9 1.0
0
0.5
[1] 5hjs.a 1.0 1.3 1.4 1.2 1.0 1.0 0.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.0 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
1uhl.b
2acl.b
2acl.d
2acl.f
3fal.b
3fc6.b
5avl.a
5hjs.a
[1] 1uhl.b
0
2.0 2.3 2.2 2.0 1.9 2.0 1.9
[1] 2acl.b 2.0
0
1.1 1.2 1.1 0.9 1.6 1.5
[1] 2acl.d 2.3 1.1
0
1.2 1.2 1.2 1.7 1.6
[1] 2acl.f 2.2 1.2 1.2
0
1.2 1.3 1.7 1.7
[1] 3fal.b 2.0 1.1 1.2 1.2
0
0.9 1.6 1.5
[1] 3fc6.b 1.9 0.9 1.2 1.3 0.9
0
1.5 1.3
[1] 5avl.a 2.0 1.6 1.7 1.7 1.6 1.5
0
0.7
[1] 5hjs.a 1.9 1.5 1.6 1.7 1.5 1.3 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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