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NR1I2_HUMAN_130_434

Nuclear receptor subfamily 1 group I member 2 [Nuclear hormone receptor family. NR1 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (NR1I2_HUMAN):D: NR LBD (205:211, 227, 228, 236:240, 242:244, 246, 247, 250, 251, 280, 281, 284, 285, 288, 299, 301, 306, 308, 323, 324, 327, 407, 408, 410, 411, 414, 420, 421, 425, 428, 429)205:211, 227, 228, 236:240, 242:244, 246, 247, 250, 251, 280, 281, 284, 285, 288, 299, 301, 306, 308, 323, 324, 327, 407, 408, 410, 411, 414, 420, 421, 425, 428, 429

Full PDB list

1ilg, 1ilh, 1m13, 1nrl, 1skx, 2o9i, 2qnv, 3ctb, 3hvl, 4j5w, 4j5x, 4ny9, 4s0s, 4s0t, 4x1f, 4x1g, 4xao, 4xhd, 5a86, 5x0r, 6bns (redundant Pocketome entry); 3r8d (unprocessed)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
D
2
0
5
L
2
0
6
C
2
0
7
L
2
0
9
K
2
1
0
V
2
1
1
P
2
2
7
I
2
3
6
L
2
3
9
L
2
4
0
H
2
4
2
M
2
4
3
A
2
4
4
M
2
4
6
S
2
4
7
F
2
5
1
A
2
8
0
F
2
8
1
C
2
8
4
Q
2
8
5
F
2
8
8
W
2
9
9
C
3
0
1
Y
3
0
6
L
3
0
8
M
3
2
3
L
3
2
4
H
3
2
7
H
4
0
7
T
4
0
8
R
4
1
0
L
4
1
1
I
4
1
4
F
4
2
0
M
4
2
5
L
4
2
8
F
4
2
9
[1]1ilg.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1m13.a hyf39 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1nrl.a srl33 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1skx.a rfp51 - - - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2o9i.b 44431 . . . . . . . . . . . . . . . . . . S . . . . . . . . . . . . . . . . . .
[1]2qnv.a cdz29 - - - . . . . - . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ny9.a 2q430 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4s0t.a 40u29 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4x1f.a 3wf22 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4x1g.a 3wf,3wg41 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5a86.a d7e28 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]6bns.a xgh39 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]5x0r.b 4wh30 - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
D
2
0
5
L
2
0
6
C
2
0
7
S
2
0
8
L
2
0
9
K
2
1
0
V
2
1
1
P
2
2
7
P
2
2
8
I
2
3
6
F
2
3
7
S
2
3
8
L
2
3
9
L
2
4
0
H
2
4
2
M
2
4
3
A
2
4
4
M
2
4
6
S
2
4
7
M
2
5
0
F
2
5
1
A
2
8
0
F
2
8
1
C
2
8
4
Q
2
8
5
F
2
8
8
W
2
9
9
C
3
0
1
Y
3
0
6
L
3
0
8
M
3
2
3
L
3
2
4
H
3
2
7
H
4
0
7
T
4
0
8
R
4
1
0
L
4
1
1
I
4
1
4
F
4
2
0
A
4
2
1
M
4
2
5
L
4
2
8
F
4
2
9
[1]1ilg.a . . . . * . . . . . . . . . . * . . . . * . . . . . . . . . . . . * . . . . * . . . .
[1]1m13.a . . . . * * . . . . . . . . . * . . . . * . . . . . . . . . . . . . . . . . * . . . .
[1]1nrl.a . . . . * * . . . . . . . . . * . . . . * . . . . . . . . . . . . . . . . . * . . . *
[1]1skx.a - - - - - . . . . . . . . . . * . . . . * . . . . . . . . . . . . * . . . . . . . . .
[1]2o9i.b . . . . * * . . . . . . . . . * . . . . * . . S . . . . . . . . . * . * * * * . . . *
[1]2qnv.a - - - - * . . . . - . . . * . * . . . . * . . . . * . . . . . . . . . . * . * . . . .
[1]4ny9.a . . . . * * . . . . . . . . . * . . . . * . . . . . . . . . * . . * . . . . . . . . .
[1]4s0t.a . . . . * * . . . . . . . . . * . . . . * . . . . . . . . . * . . * . . . . . . . . *
[1]4x1f.a . . . . * * . . . . . . . . . * . . . . * . . . . . . . . . . . . . . . . . * . . . *
[1]4x1g.a . . . . * * . . . . . . . . . * . . . . * . . . . . . . . . . . . * . . . . * . . . *
[1]5a86.a . . . . * * . . . . . . . . . * . . . . * . . . . . . . . . . . . * . . . . * . . . *
[1]6bns.a . . . . * * . . . . . . . . . * . . . . * . . . . . . . . . . . . * . . . . * . . . *
[2]5x0r.b - - . . * * . . . . . . . . . * . . . . . . . . . . . . . . * . . * . . * . * . . . .

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
1ilg.a is apo
1m13.a:hyf
1nrl.a:srl
1skx.a:rfp
2o9i.b:444
2qnv.a:cdz
4ny9.a:2q4
4s0t.a:40u
4x1f.a:3wf
4x1g.a:3wf,3wg
5a86.a:d7e
6bns.a:xgh
5x0r.b:4wh
[1] 1ilg.a
-
3.0 2.1 5.6 0.4 2.1 1.5 1.8 1.3 1.3 2.3 2.5 3.4
[1] 1m13.a -
0.3
0.9 4.1 0 1.2 0.9 1.2 0.6 1.0 2.0 0.6 2.7
[1] 1nrl.a - 1.1
0
5.3 0.7 0.6 0.9 1.6 0.8 1.3 1.8 0.8 4.1
[1] 1skx.a - 2.2 1.9
0
0.8 1.5 1.1 1.2 0.9 1.1 2.0 0 3.6
[1] 2o9i.b - 1.7 2.1 6.1
0
1.7 1.0 1.5 1.3 1.7 2.3 2.1 5.0
[1] 2qnv.a - 3.1 3.4 5.4 1.9
0.3
2.7 3.1 1.0 2.8 4.0 2.8 4.0
[1] 4ny9.a - 1.8 2.5 5.0 0.6 1.1
0
0.1 1.7 1.8 2.4 2.3 4.6
[1] 4s0t.a - 1.9 2.4 4.6 0.7 1.7 0
0
1.2 1.8 3.0 1.3 5.5
[1] 4x1f.a - 1.8 0.8 4.9 0.3 0.6 1.5 2.0
0
0 1.4 0.4 3.9
[1] 4x1g.a - 2.5 0.7 4.4 0.1 0.8 1.3 1.5 0
0.1
1.7 0.5 4.0
[1] 5a86.a - 4.8 2.9 6.4 2.9 4.3 2.9 4.1 5.8 5.7
0.1
4.1 5.3
[1] 6bns.a - 0.8 2.2 3.8 0.4 1.0 1.1 1.8 1.2 1.2 1.9
0.1
5.2
[2] 5x0r.b - 4.5 4.0 6.3 1.3 2.9 2.4 1.9 1.8 2.7 3.0 2.4
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
1ilg.a
1m13.a
1nrl.a
1skx.a
2o9i.b
2qnv.a
4ny9.a
4s0t.a
4x1f.a
4x1g.a
5a86.a
6bns.a
5x0r.b
[1] 1ilg.a
0
.11 .16 .17 .14 .19 .15 .21 .15 .15 .14 .15 .27
[1] 1m13.a .11
0
.10 .17 .12 .13 .15 .19 .11 .12 .13 .12 .25
[1] 1nrl.a .16 .10
0
.21 .16 .19 .17 .20 .11 .13 .10 .12 .28
[1] 1skx.a .17 .17 .21
0
.22 .22 .20 .22 .17 .15 .18 .13 .30
[1] 2o9i.b .14 .12 .16 .22
0
.20 .17 .19 .15 .15 .13 .15 .25
[1] 2qnv.a .19 .13 .19 .22 .20
0
.23 .26 .19 .21 .20 .20 .25
[1] 4ny9.a .15 .15 .17 .20 .17 .23
0
.10 .18 .17 .16 .17 .26
[1] 4s0t.a .21 .19 .20 .22 .19 .26 .10
0
.21 .20 .15 .18 .20
[1] 4x1f.a .15 .11 .11 .17 .15 .19 .18 .21
0
.04 .13 .09 .28
[1] 4x1g.a .15 .12 .13 .15 .15 .21 .17 .20 .04
0
.13 .09 .27
[1] 5a86.a .14 .13 .10 .18 .13 .20 .16 .15 .13 .13
0
.07 .25
[1] 6bns.a .15 .12 .12 .13 .15 .20 .17 .18 .09 .09 .07
0
.24
[2] 5x0r.b .27 .25 .28 .30 .25 .25 .26 .20 .28 .27 .25 .24
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.2 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
1ilg.a
1m13.a
1nrl.a
1skx.a
2o9i.b
2qnv.a
4ny9.a
4s0t.a
4x1f.a
4x1g.a
5a86.a
6bns.a
5x0r.b
[1] 1ilg.a
0
0.5 0.7 0.4 0.9 0.8 0.6 0.8 0.5 0.5 0.8 0.6 0.8
[1] 1m13.a 0.5
0
0.7 0.5 0.9 0.8 0.7 0.8 0.5 0.5 0.9 0.5 0.9
[1] 1nrl.a 0.7 0.7
0
0.7 0.7 0.9 0.5 0.6 0.4 0.5 0.9 0.5 0.6
[1] 1skx.a 0.4 0.5 0.7
0
0.8 0.7 0.5 0.7 0.6 0.5 0.7 0.6 0.8
[1] 2o9i.b 0.9 0.9 0.7 0.8
0
0.9 0.6 0.5 0.8 0.8 1.3 0.9 0.8
[1] 2qnv.a 0.8 0.8 0.9 0.7 0.9
0
0.8 0.8 0.8 0.8 1.3 0.9 0.8
[1] 4ny9.a 0.6 0.7 0.5 0.5 0.6 0.8
0
0.4 0.5 0.5 1.0 0.6 0.6
[1] 4s0t.a 0.8 0.8 0.6 0.7 0.5 0.8 0.4
0
0.6 0.7 1.2 0.8 0.6
[1] 4x1f.a 0.5 0.5 0.4 0.6 0.8 0.8 0.5 0.6
0
0.1 0.8 0.4 0.7
[1] 4x1g.a 0.5 0.5 0.5 0.5 0.8 0.8 0.5 0.7 0.1
0
0.8 0.4 0.7
[1] 5a86.a 0.8 0.9 0.9 0.7 1.3 1.3 1.0 1.2 0.8 0.8
0
0.8 1.1
[1] 6bns.a 0.6 0.5 0.5 0.6 0.9 0.9 0.6 0.8 0.4 0.4 0.8
0
0.8
[2] 5x0r.b 0.8 0.9 0.6 0.8 0.8 0.8 0.6 0.6 0.7 0.7 1.1 0.8
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
1ilg.a
1m13.a
1nrl.a
1skx.a
2o9i.b
2qnv.a
4ny9.a
4s0t.a
4x1f.a
4x1g.a
5a86.a
6bns.a
5x0r.b
[1] 1ilg.a
0
0.8 1.1 0.8 1.2 1.4 1.2 1.4 0.9 0.9 1.3 0.7 1.4
[1] 1m13.a 0.8
0
0.8 1.0 1.2 1.3 1.3 1.4 0.8 0.8 1.4 0.9 1.4
[1] 1nrl.a 1.1 0.8
0
1.2 1.1 1.5 1.2 1.3 0.8 0.8 1.4 1.0 1.3
[1] 1skx.a 0.8 1.0 1.2
0
1.1 1.2 1.3 1.2 0.9 0.9 1.3 0.8 1.2
[1] 2o9i.b 1.2 1.2 1.1 1.1
0
1.5 1.1 1.1 1.2 1.2 1.7 1.0 1.2
[1] 2qnv.a 1.4 1.3 1.5 1.2 1.5
0
1.8 1.7 1.3 1.3 1.9 1.4 1.3
[1] 4ny9.a 1.2 1.3 1.2 1.3 1.1 1.8
0
0.8 1.1 1.1 1.6 1.0 1.3
[1] 4s0t.a 1.4 1.4 1.3 1.2 1.1 1.7 0.8
0
1.2 1.2 1.6 1.2 1.4
[1] 4x1f.a 0.9 0.8 0.8 0.9 1.2 1.3 1.1 1.2
0
0.2 1.2 0.9 1.3
[1] 4x1g.a 0.9 0.8 0.8 0.9 1.2 1.3 1.1 1.2 0.2
0
1.2 0.9 1.3
[1] 5a86.a 1.3 1.4 1.4 1.3 1.7 1.9 1.6 1.6 1.2 1.2
0
1.2 1.7
[1] 6bns.a 0.7 0.9 1.0 0.8 1.0 1.4 1.0 1.2 0.9 0.9 1.2
0
1.2
[2] 5x0r.b 1.4 1.4 1.3 1.2 1.2 1.3 1.3 1.4 1.3 1.3 1.7 1.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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