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RORG_HUMAN_483_511

Nuclear receptor ROR-gamma [Nuclear hormone receptor family. NR1 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (RORG_HUMAN):D: NR LBD (317, 318, 320:322, 324, 325, 328, 329, 332, 353:355, 357, 358, 476, 479, 480, 483, 484, 486, 487, 492, 494:503, 505, 506)317, 318, 320:322, 324, 325, 328, 329, 332, 353:355, 357, 358, 476, 479, 480, 483, 484, 486, 487, 492, 494:503, 505, 506

Full PDB list

4qm0, 4wlb, 4wqp, 4ypq, 5apk, 5c4o, 5c4s, 5c4t, 5c4u, 5ejv, 5iz0, 5k6e, 5lwp, 5ntn, 5nu1 (redundant Pocketome entry); 3b0w, 3kyt, 3l0j, 3l0l, 4nb6, 4nie, 4wpf, 4xt9, 4ymq, 5aph, 5apj, 5ayg, 5g42, 5g43, 5g44, 5g45, 5g46, 5k38, 5k3l, 5k3m, 5k3n, 5k74, 5nti, 5ntp, 5ntq, 5ntw, 5ufo, 5ufr, 5uhi, 5vb3, 5vb5, 5vb6, 5vb7, 5x8q, 5x8s, 5x8u, 5x8w, 5x8x, 5yp6, 6bn6 (unprocessed)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
W
3
1
7
A
3
2
1
L
3
2
4
T
3
2
5
I
3
2
8
Q
3
2
9
L
3
5
3
K
3
5
4
A
3
5
7
M
3
5
8
C
4
7
6
V
4
8
0
L
4
8
3
Q
4
8
4
Q
4
8
7
I
4
9
2
V
4
9
4
A
4
9
6
A
4
9
7
F
4
9
8
L
5
0
1
Y
5
0
2
L
5
0
5
F
5
0
6
[1]5c4o.a 4f131 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5c4s.a 4y533 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5c4t.a 4y633 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5c4u.a 4y733 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5lwp.a 79u35 . . . . . . . . . . . . . . . . . . . . . . . .
[2]4wlb.a none . . . . . . . . . . . . . . . . . . . . . . . .

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
W
3
1
7
E
3
1
8
C
3
2
0
A
3
2
1
H
3
2
2
L
3
2
4
T
3
2
5
I
3
2
8
Q
3
2
9
V
3
3
2
L
3
5
3
K
3
5
4
A
3
5
5
A
3
5
7
M
3
5
8
C
4
7
6
H
4
7
9
V
4
8
0
L
4
8
3
Q
4
8
4
F
4
8
6
Q
4
8
7
I
4
9
2
V
4
9
4
Q
4
9
5
A
4
9
6
A
4
9
7
F
4
9
8
P
4
9
9
P
5
0
0
L
5
0
1
Y
5
0
2
K
5
0
3
L
5
0
5
F
5
0
6
[1]5c4o.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5c4s.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5c4t.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5c4u.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5lwp.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4wlb.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
5c4o.a:4f1
5c4s.a:4y5
5c4t.a:4y6
5c4u.a:4y7
5lwp.a:79u
4wlb.a is apo
[1] 5c4o.a
0
0 0 0 0.2 -
[1] 5c4s.a 0
0
0 0 0.1 -
[1] 5c4t.a 0.2 0
0
0.1 0.3 -
[1] 5c4u.a 0 0.1 0.1
0
0.2 -
[1] 5lwp.a 0 0 0 0
0
-
[2] 4wlb.a 12 13 14 12 14
-
[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
5c4o.a
5c4s.a
5c4t.a
5c4u.a
5lwp.a
4wlb.a
[1] 5c4o.a
0
0 .01 0 0 .42
[1] 5c4s.a 0
0
.01 .01 0 .42
[1] 5c4t.a .01 .01
0
.01 .01 .42
[1] 5c4u.a 0 .01 .01
0
.01 .42
[1] 5lwp.a 0 0 .01 .01
0
.42
[2] 4wlb.a .42 .42 .42 .42 .42
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
5c4o.a
5c4s.a
5c4t.a
5c4u.a
5lwp.a
4wlb.a
[1] 5c4o.a
0
0.1 0.9 0.3 0.3 7.2
[1] 5c4s.a 0.1
0
0.9 0.3 0.3 7.2
[1] 5c4t.a 0.9 0.9
0
1.0 0.9 6.7
[1] 5c4u.a 0.3 0.3 1.0
0
0.3 7.2
[1] 5lwp.a 0.3 0.3 0.9 0.3
0
7.2
[2] 4wlb.a 7.2 7.2 6.7 7.2 7.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
5c4o.a
5c4s.a
5c4t.a
5c4u.a
5lwp.a
4wlb.a
[1] 5c4o.a
0
0.2 1.6 0.6 0.8 7.9
[1] 5c4s.a 0.2
0
1.6 0.5 0.8 8.0
[1] 5c4t.a 1.6 1.6
0
1.7 1.6 7.4
[1] 5c4u.a 0.6 0.5 1.7
0
0.8 7.9
[1] 5lwp.a 0.8 0.8 1.6 0.8
0
7.9
[2] 4wlb.a 7.9 8.0 7.4 7.9 7.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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