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NR1H3_HUMAN_189_447_ligBind

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 (225, 228, 229, 232, 254, 257, 258, 260, 261, 263, 264, 267, 295, 298, 299, 301, 302, 305, 313, 315:317, 326, 329:331, 335, 336, 339, 340, 421, 424, 425, 428, 435, 439, 443)
D: NR LBD (225, 228, 229, 232, 254, 257, 258, 260, 261, 263, 264, 267, 295, 298, 299, 301, 302, 305, 313, 315:317, 326, 329:331, 335, 336, 339, 340, 421, 424, 425, 428, 435, 439, 443)
225, 228, 229, 232, 254, 257, 258, 260, 261, 263, 264, 267, 295, 298, 299, 301, 302, 305, 313, 315:317, 326, 329:331, 335, 336, 339, 340, 421, 424, 425, 428, 435, 439, 443

Full PDB list

1uhl, 2acl, 3fal, 3fc6, 3ipq, 3ips, 3ipu, 5avi, 5avl, 5hjs

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
N
2
2
5
R
2
3
2
F
2
5
4
F
2
5
7
T
2
5
8
L
2
6
0
A
2
6
1
V
2
6
3
S
2
6
4
E
2
6
7
I
2
9
5
M
2
9
8
L
2
9
9
E
3
0
1
T
3
0
2
R
3
0
5
I
3
1
3
F
3
1
5
L
3
1
6
F
3
2
6
A
3
2
9
G
3
3
0
L
3
3
1
F
3
3
5
I
3
3
6
I
3
3
9
F
3
4
0
H
4
2
1
Q
4
2
4
L
4
2
8
L
4
3
5
L
4
3
9
W
4
4
3
[1]1uhl.b 44431 . - . . . . . . . . . . . . . . . - - . . . . . . . . . . . . . .
[1]2acl.f l0529 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3fal.b lo233 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3fc6.b lx244 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3ipq.a 96541 - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3ips.b o9032 - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3ipu.a o4034 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5avi.c 4km30 - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5avl.a 4kq36 - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5hjs.a 66835 - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
N
2
2
5
S
2
2
8
F
2
2
9
R
2
3
2
F
2
5
4
F
2
5
7
T
2
5
8
L
2
6
0
A
2
6
1
V
2
6
3
S
2
6
4
E
2
6
7
I
2
9
5
M
2
9
8
L
2
9
9
E
3
0
1
T
3
0
2
R
3
0
5
I
3
1
3
F
3
1
5
L
3
1
6
K
3
1
7
F
3
2
6
A
3
2
9
G
3
3
0
L
3
3
1
F
3
3
5
I
3
3
6
I
3
3
9
F
3
4
0
H
4
2
1
Q
4
2
4
V
4
2
5
L
4
2
8
L
4
3
5
L
4
3
9
W
4
4
3
[1]1uhl.b . . . - . . . . . . . . . . . . . . . - - - * . . . . . . . . . . . . . .
[1]2acl.f . . . . . . . . . . . . . . . . . . . . * . * . . . . . . . . . . . . . .
[1]3fal.b . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . * . . .
[1]3fc6.b . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . .
[1]3ipq.a - - - - . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . .
[1]3ips.b - - - - . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . .
[1]3ipu.a . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . .
[1]5avi.c - - - - . . . . . . . . . . . . . . . . * * * . . * . . . . . . . . . . .
[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:444
2acl.f:l05
3fal.b:lo2
3fc6.b:lx2
3ipq.a:965
3ips.b:o90
3ipu.a:o40
5avi.c:4km
5avl.a:4kq
5hjs.a:668
[1] 1uhl.b
0.2
1.0 1.6 2.4 2.0 0.4 0.5 0.2 0.8 0.5
[1] 2acl.f 0.8
0
1.4 2.6 1.9 1.7 2.4 0.1 0.4 0.8
[1] 3fal.b 1.4 2.1
0.2
0.5 0.5 2.9 3.0 0.7 0.7 1.0
[1] 3fc6.b 0.8 1.0 0.2
0
0 2.1 2.6 0.5 0.5 0.8
[1] 3ipq.a 0.9 1.5 0.1 0.2
0
1.9 2.7 0.4 0.8 0.8
[1] 3ips.b 0.5 0.9 1.4 1.9 1.6
0
0.5 0.1 0.4 0.4
[1] 3ipu.a 0.7 0.4 1.4 2.1 2.1 0.7
0
0 0.1 0.7
[1] 5avi.c 0.8 0.3 1.7 2.6 2.1 0.9 1.9
0
0.6 0.8
[1] 5avl.a 1.5 0.8 1.9 2.6 2.4 1.8 2.1 0.2
0
1.0
[1] 5hjs.a 1.0 0.9 1.4 1.9 1.8 2.5 2.2 0.3 0.6
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.f
3fal.b
3fc6.b
3ipq.a
3ips.b
3ipu.a
5avi.c
5avl.a
5hjs.a
[1] 1uhl.b
0
.12 .20 .18 .18 .09 .10 .12 .18 .15
[1] 2acl.f .12
0
.18 .14 .14 .10 .13 .10 .11 .09
[1] 3fal.b .20 .18
0
.08 .08 .18 .22 .22 .15 .13
[1] 3fc6.b .18 .14 .08
0
.06 .14 .17 .17 .12 .08
[1] 3ipq.a .18 .14 .08 .06
0
.15 .20 .18 .13 .12
[1] 3ips.b .09 .10 .18 .14 .15
0
.06 .09 .11 .09
[1] 3ipu.a .10 .13 .22 .17 .20 .06
0
.10 .13 .12
[1] 5avi.c .12 .10 .22 .17 .18 .09 .10
0
.10 .12
[1] 5avl.a .18 .11 .15 .12 .13 .11 .13 .10
0
.08
[1] 5hjs.a .15 .09 .13 .08 .12 .09 .12 .12 .08
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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.f
3fal.b
3fc6.b
3ipq.a
3ips.b
3ipu.a
5avi.c
5avl.a
5hjs.a
[1] 1uhl.b
0
1.3 1.2 1.2 0.7 0.8 1.4 0.9 0.9 0.8
[1] 2acl.f 1.3
0
0.9 0.7 0.7 0.5 1.0 0.5 0.5 0.4
[1] 3fal.b 1.2 0.9
0
0.6 0.6 0.9 1.4 0.9 0.9 0.8
[1] 3fc6.b 1.2 0.7 0.6
0
0.3 0.8 1.2 0.8 0.8 0.6
[1] 3ipq.a 0.7 0.7 0.6 0.3
0
0.7 1.1 0.7 0.8 0.5
[1] 3ips.b 0.8 0.5 0.9 0.8 0.7
0
0.8 0.4 0.5 0.4
[1] 3ipu.a 1.4 1.0 1.4 1.2 1.1 0.8
0
0.7 0.6 0.8
[1] 5avi.c 0.9 0.5 0.9 0.8 0.7 0.4 0.7
0
0.4 0.4
[1] 5avl.a 0.9 0.5 0.9 0.8 0.8 0.5 0.6 0.4
0
0.5
[1] 5hjs.a 0.8 0.4 0.8 0.6 0.5 0.4 0.8 0.4 0.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 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
1uhl.b
2acl.f
3fal.b
3fc6.b
3ipq.a
3ips.b
3ipu.a
5avi.c
5avl.a
5hjs.a
[1] 1uhl.b
0
2.1 2.0 2.0 1.6 1.6 2.1 1.6 1.6 1.5
[1] 2acl.f 2.1
0
1.2 1.0 1.1 0.9 1.7 1.0 1.2 0.8
[1] 3fal.b 2.0 1.2
0
0.8 0.8 1.2 2.0 1.1 1.2 1.0
[1] 3fc6.b 2.0 1.0 0.8
0
0.7 1.1 1.9 1.1 1.3 0.9
[1] 3ipq.a 1.6 1.1 0.8 0.7
0
1.0 1.2 1.0 1.1 0.8
[1] 3ips.b 1.6 0.9 1.2 1.1 1.0
0
0.7 0.8 0.9 0.7
[1] 3ipu.a 2.1 1.7 2.0 1.9 1.2 0.7
0
1.0 1.0 1.0
[1] 5avi.c 1.6 1.0 1.1 1.1 1.0 0.8 1.0
0
0.9 0.8
[1] 5avl.a 1.6 1.2 1.2 1.3 1.1 0.9 1.0 0.9
0
1.0
[1] 5hjs.a 1.5 0.8 1.0 0.9 0.8 0.7 1.0 0.8 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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