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PRGR_HUMAN_677_933

Progesterone receptor [Nuclear hormone receptor family. NR3 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PRGR_HUMAN):D: NR LBD (715, 718, 719, 721:723, 725, 726, 755, 756, 759, 760, 763, 766, 778, 794, 797, 798, 801, 887, 888, 890, 891, 894, 903, 905, 908, 909, 912, 913)
R: AF2
mediates transcriptional activation (715, 718, 719, 721:723, 725, 726, 755, 756, 759, 760, 763, 766, 778, 794, 797, 798, 801, 887, 888, 890, 891, 894, 903, 905, 908, 909, 912, 913, 917, 919)
715, 718, 719, 721:723, 725, 726, 755, 756, 759, 760, 763, 766, 778, 794, 797, 798, 801, 887, 888, 890, 891, 894, 903, 905, 908, 909, 912, 913, 917, 919

Full PDB list

1a28, 1e3k, 1sqn, 1sr7, 1zuc, 2ovh, 2ovm, 2w8y, 3d90, 3g8o, 3hq5, 3kba, 3zr7, 3zra, 3zrb, 4a2j, 4apu, 4oar (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
7
1
5
L
7
1
8
N
7
1
9
L
7
2
1
G
7
2
2
E
7
2
3
Q
7
2
5
L
7
2
6
W
7
5
5
M
7
5
6
M
7
5
9
V
7
6
0
L
7
6
3
R
7
6
6
F
7
7
8
F
7
9
4
L
7
9
7
C
7
9
8
M
8
0
1
L
8
8
7
Y
8
9
0
C
8
9
1
T
8
9
4
V
9
0
3
F
9
0
5
M
9
0
9
V
9
1
2
I
9
1
3
[1]1a28.b str23 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1e3k.a r1821 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1sr7.a mof35 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1zuc.b t9821 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2w8y.a 48632 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2w8y.b ndr22 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3d90.b nog23 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3g8o.a 30x25 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3hq5.a gkk27 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3kba.a wow27 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3zr7.a or826 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3zra.b orb27 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3zrb.b orc26 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4a2j.b as033 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4apu.b a2k38 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4oar.a 2s035 . . . . . . . . . . . . . . . . . . . . . . . - - . . .

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
L
7
1
5
L
7
1
8
N
7
1
9
L
7
2
1
G
7
2
2
E
7
2
3
Q
7
2
5
L
7
2
6
W
7
5
5
M
7
5
6
M
7
5
9
V
7
6
0
L
7
6
3
R
7
6
6
F
7
7
8
F
7
9
4
L
7
9
7
C
7
9
8
M
8
0
1
L
8
8
7
H
8
8
8
Y
8
9
0
C
8
9
1
T
8
9
4
V
9
0
3
F
9
0
5
M
9
0
8
M
9
0
9
V
9
1
2
I
9
1
3
L
9
1
7
K
9
1
9
[1]1a28.b . . . . . . . . * . . . . . . * * . . . . . . . . . . * . . . .
[1]1e3k.a . . . . . . . . * . * . . . . * * . . . . * . . . . . * . . . .
[1]1sr7.a . . . . . . . . * . . . . . . . . . . . . . . . . . . * . . . .
[1]1zuc.b . . . . . . . . * . . . . . . * * . . . . . . . . . . * . . . .
[1]2w8y.a . . . . . . . . * . . . . . . * * . . . . . . . . . . . . . . .
[1]2w8y.b . . . . . . . . * . . . . . . * * . . . . . . . . . . * . . . .
[1]3d90.b . . . . . . . . * . . . . . . * * . . . . . . . . . . * . . . .
[1]3g8o.a . . . . . . . . * . . . . . . * * . . . . * . . . . . * . . . .
[1]3hq5.a . . . . . . . . * . * . . . . . . . . . . . . . . . . * . . . .
[1]3kba.a . . . . . . . . * . * . . . . * . . . . . . . . . . . * . . . .
[1]3zr7.a . . . . . . . . * . . . . . . * * . . . . * . . . . . * . . . .
[1]3zra.b . . . . . . . . * . * . . . . * * . . . . * . . . . . * . . . .
[1]3zrb.b . . . . . . . . * . . . . . . * * . . . . * . . . . . * . . . .
[1]4a2j.b . . . . . . . . * . . . . . . * * . . . . . . . . . . . . . . .
[1]4apu.b * . . . . . . . * . . . . . . * . . . . . . . . . . . * . . . .
[1]4oar.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
1a28.b:str
1e3k.a:r18
1sr7.a:mof
1zuc.b:t98
2w8y.a:486
2w8y.b:ndr
3d90.b:nog
3g8o.a:30x
3hq5.a:gkk
3kba.a:wow
3zr7.a:or8
3zra.b:orb
3zrb.b:orc
4a2j.b:as0
4apu.b:a2k
4oar.a:2s0
[1] 1a28.b
0
0.2 1.5 0.1 2.2 0.1 0.3 0.3 0.8 0.8 0.4 1.3 0.7 1.5 5.1 3.4
[1] 1e3k.a 0.4
0.1
3.4 0 3.3 0.1 0.4 0.3 0.9 1.0 0.3 0.9 0.6 2.1 4.9 4.5
[1] 1sr7.a 0.1 0.3
0
0.1 2.2 0.1 0.3 0.5 0.3 0.3 0.5 1.2 1.0 1.7 4.8 2.9
[1] 1zuc.b 0.3 0.4 2.3
0
3.2 0.2 0.2 0.3 1.0 0.9 0.7 1.7 0.7 2.7 5.3 4.0
[1] 2w8y.a 0.1 0.4 2.0 0.2
0.1
0 0.1 0 1.0 1.1 0.1 0.6 0.2 0.3 4.8 0.7
[1] 2w8y.b 0.1 0.3 2.1 0.3 2.8
0
0.1 0.1 0.8 1.1 0.1 0.5 0.4 2.6 5.4 3.7
[1] 3d90.b 0.1 0.1 2.6 0 2.9 0
0
0 0.4 0.9 0.1 0.6 0 3.0 4.7 3.6
[1] 3g8o.a 0.4 0.2 3.2 0.1 2.8 0 0.1
0
0.7 0.9 0.3 0.5 0.4 2.0 3.7 3.9
[1] 3hq5.a 0.9 0.2 2.6 0 3.5 0.3 0.1 0.1
0
0.2 0.8 0.8 0.9 3.4 3.9 4.4
[1] 3kba.a 0.8 0.1 3.1 0 3.6 0.3 0.1 0.1 0
0
0.6 0.7 0.5 3.1 3.9 4.4
[1] 3zr7.a 0.5 0.3 2.1 0.4 1.9 0.1 0.4 0 1.0 1.4
0
0.5 0.1 2.2 5.9 3.6
[1] 3zra.b 1.1 0.1 3.9 0.4 2.4 0.1 0.3 0.1 1.0 1.6 0.4
0
0.1 2.0 5.6 3.4
[1] 3zrb.b 0.5 0.2 2.3 0.4 2.2 0.1 0.3 0.1 1.2 1.4 0.1 0.3
0.1
2.2 6.0 3.5
[1] 4a2j.b 0 0.2 1.8 0.1 0.5 0 0.3 0.1 0.9 0.7 0.2 0.4 0.3
0.1
5.0 1.5
[1] 4apu.b 0.1 0.3 1.5 0.1 3.0 0.2 0.3 0.1 0.3 0.3 0.2 1.0 0.3 2.0
0
4.1
[1] 4oar.a 0.2 0.2 2.0 0.1 0 0.1 0.2 0.1 1.0 1.0 0 0 0.2 0.3 4.6
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
1a28.b
1e3k.a
1sr7.a
1zuc.b
2w8y.a
2w8y.b
3d90.b
3g8o.a
3hq5.a
3kba.a
3zr7.a
3zra.b
3zrb.b
4a2j.b
4apu.b
4oar.a
[1] 1a28.b
0
.11 .09 .08 .10 .08 .08 .14 .17 .15 .07 .13 .10 .09 .15 .18
[1] 1e3k.a .11
0
.17 .12 .17 .10 .07 .10 .16 .12 .13 .10 .13 .16 .19 .20
[1] 1sr7.a .09 .17
0
.17 .15 .14 .13 .18 .17 .17 .14 .18 .14 .14 .17 .21
[1] 1zuc.b .08 .12 .17
0
.16 .13 .10 .17 .19 .17 .12 .19 .15 .14 .20 .23
[1] 2w8y.a .10 .17 .15 .16
0
.12 .13 .18 .21 .18 .13 .17 .16 .07 .17 .08
[1] 2w8y.b .08 .10 .14 .13 .12
0
.08 .14 .18 .17 .08 .10 .07 .12 .19 .16
[1] 3d90.b .08 .07 .13 .10 .13 .08
0
.12 .18 .13 .12 .13 .13 .14 .19 .19
[1] 3g8o.a .14 .10 .18 .17 .18 .14 .12
0
.12 .11 .14 .10 .17 .17 .15 .20
[1] 3hq5.a .17 .16 .17 .19 .21 .18 .18 .12
0
.05 .18 .16 .19 .19 .16 .23
[1] 3kba.a .15 .12 .17 .17 .18 .17 .13 .11 .05
0
.18 .13 .20 .18 .15 .20
[1] 3zr7.a .07 .13 .14 .12 .13 .08 .12 .14 .18 .18
0
.10 .07 .11 .22 .19
[1] 3zra.b .13 .10 .18 .19 .17 .10 .13 .10 .16 .13 .10
0
.11 .14 .23 .17
[1] 3zrb.b .10 .13 .14 .15 .16 .07 .13 .17 .19 .20 .07 .11
0
.14 .22 .18
[1] 4a2j.b .09 .16 .14 .14 .07 .12 .14 .17 .19 .18 .11 .14 .14
0
.16 .11
[1] 4apu.b .15 .19 .17 .20 .17 .19 .19 .15 .16 .15 .22 .23 .22 .16
0
.20
[1] 4oar.a .18 .20 .21 .23 .08 .16 .19 .20 .23 .20 .19 .17 .18 .11 .20
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
1a28.b
1e3k.a
1sr7.a
1zuc.b
2w8y.a
2w8y.b
3d90.b
3g8o.a
3hq5.a
3kba.a
3zr7.a
3zra.b
3zrb.b
4a2j.b
4apu.b
4oar.a
[1] 1a28.b
0
0.4 0.3 0.3 0.3 0.4 0.3 0.5 0.5 0.5 0.2 0.4 0.3 0.5 0.5 4.7
[1] 1e3k.a 0.4
0
0.4 0.4 0.4 0.3 0.4 0.4 0.4 0.4 0.4 0.4 0.5 0.5 0.5 4.7
[1] 1sr7.a 0.3 0.4
0
0.4 0.5 0.4 0.4 0.5 0.6 0.5 0.4 0.4 0.4 0.5 0.6 4.7
[1] 1zuc.b 0.3 0.4 0.4
0
0.3 0.4 0.3 0.4 0.5 0.5 0.4 0.5 0.5 0.6 0.4 4.7
[1] 2w8y.a 0.3 0.4 0.5 0.3
0
0.4 0.3 0.5 0.6 0.6 0.3 0.4 0.4 0.5 0.5 4.6
[1] 2w8y.b 0.4 0.3 0.4 0.4 0.4
0
0.4 0.2 0.3 0.3 0.4 0.2 0.5 0.4 0.6 4.7
[1] 3d90.b 0.3 0.4 0.4 0.3 0.3 0.4
0
0.5 0.5 0.5 0.3 0.5 0.5 0.5 0.5 4.7
[1] 3g8o.a 0.5 0.4 0.5 0.4 0.5 0.2 0.5
0
0.3 0.3 0.5 0.3 0.6 0.5 0.6 4.7
[1] 3hq5.a 0.5 0.4 0.6 0.5 0.6 0.3 0.5 0.3
0
0.2 0.6 0.4 0.7 0.5 0.6 4.7
[1] 3kba.a 0.5 0.4 0.5 0.5 0.6 0.3 0.5 0.3 0.2
0
0.6 0.4 0.7 0.5 0.6 4.7
[1] 3zr7.a 0.2 0.4 0.4 0.4 0.3 0.4 0.3 0.5 0.6 0.6
0
0.4 0.2 0.5 0.5 4.7
[1] 3zra.b 0.4 0.4 0.4 0.5 0.4 0.2 0.5 0.3 0.4 0.4 0.4
0
0.4 0.3 0.6 4.7
[1] 3zrb.b 0.3 0.5 0.4 0.5 0.4 0.5 0.5 0.6 0.7 0.7 0.2 0.4
0
0.6 0.6 4.7
[1] 4a2j.b 0.5 0.5 0.5 0.6 0.5 0.4 0.5 0.5 0.5 0.5 0.5 0.3 0.6
0
0.6 4.5
[1] 4apu.b 0.5 0.5 0.6 0.4 0.5 0.6 0.5 0.6 0.6 0.6 0.5 0.6 0.6 0.6
0
4.5
[1] 4oar.a 4.7 4.7 4.7 4.7 4.6 4.7 4.7 4.7 4.7 4.7 4.7 4.7 4.7 4.5 4.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
1a28.b
1e3k.a
1sr7.a
1zuc.b
2w8y.a
2w8y.b
3d90.b
3g8o.a
3hq5.a
3kba.a
3zr7.a
3zra.b
3zrb.b
4a2j.b
4apu.b
4oar.a
[1] 1a28.b
0
0.7 0.8 0.6 0.6 0.7 0.6 1.0 1.1 1.1 0.5 0.8 0.6 0.8 1.1 5.2
[1] 1e3k.a 0.7
0
1.1 0.8 0.8 0.6 0.8 1.0 1.0 1.0 0.8 0.7 0.9 0.8 1.2 5.3
[1] 1sr7.a 0.8 1.1
0
0.9 1.1 0.9 0.9 1.1 1.1 1.1 1.0 1.0 1.0 1.0 1.2 5.3
[1] 1zuc.b 0.6 0.8 0.9
0
0.8 0.8 0.6 1.0 0.9 0.9 0.8 0.9 0.8 0.9 1.2 5.3
[1] 2w8y.a 0.6 0.8 1.1 0.8
0
0.8 0.7 1.1 1.1 1.1 0.6 0.9 0.7 0.8 1.1 4.4
[1] 2w8y.b 0.7 0.6 0.9 0.8 0.8
0
0.8 1.0 1.0 1.0 0.7 0.5 0.8 0.6 1.2 5.3
[1] 3d90.b 0.6 0.8 0.9 0.6 0.7 0.8
0
1.0 1.0 1.0 0.7 0.9 0.8 1.0 1.2 5.3
[1] 3g8o.a 1.0 1.0 1.1 1.0 1.1 1.0 1.0
0
0.7 0.7 1.1 0.9 1.2 1.1 1.1 5.2
[1] 3hq5.a 1.1 1.0 1.1 0.9 1.1 1.0 1.0 0.7
0
0.3 1.2 1.0 1.2 1.1 1.2 5.3
[1] 3kba.a 1.1 1.0 1.1 0.9 1.1 1.0 1.0 0.7 0.3
0
1.2 1.0 1.2 1.1 1.1 5.3
[1] 3zr7.a 0.5 0.8 1.0 0.8 0.6 0.7 0.7 1.1 1.2 1.2
0
0.7 0.3 0.8 1.1 5.3
[1] 3zra.b 0.8 0.7 1.0 0.9 0.9 0.5 0.9 0.9 1.0 1.0 0.7
0
0.8 0.6 1.2 5.3
[1] 3zrb.b 0.6 0.9 1.0 0.8 0.7 0.8 0.8 1.2 1.2 1.2 0.3 0.8
0
0.8 1.2 5.3
[1] 4a2j.b 0.8 0.8 1.0 0.9 0.8 0.6 1.0 1.1 1.1 1.1 0.8 0.6 0.8
0
1.2 5.0
[1] 4apu.b 1.1 1.2 1.2 1.2 1.1 1.2 1.2 1.1 1.2 1.1 1.1 1.2 1.2 1.2
0
5.2
[1] 4oar.a 5.2 5.3 5.3 5.3 4.4 5.3 5.3 5.2 5.3 5.3 5.3 5.3 5.3 5.0 5.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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