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NR1D2_HUMAN_385_579_ligBind

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (NR1D2_HUMAN):D: NR LBD (381:386, 399, 402, 405, 406, 409, 410, 413, 443, 446, 447, 450, 454, 479:484, 486, 568, 571:575)
R: Interaction with ZNHIT1 (399, 402, 405, 406, 409, 410, 413, 443, 446, 447, 450, 454, 479:484, 486, 568, 571:575)
381:386, 399, 402, 405, 406, 409, 410, 413, 443, 446, 447, 450, 454, 479:484, 486, 568, 571:575

Full PDB list

2v0v, 2v7c, 3cqv, 4n73

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
H
3
8
1
L
3
8
2
V
3
8
3
C
3
8
4
P
3
8
5
L
3
8
6
W
4
0
2
F
4
0
5
F
4
0
9
V
4
1
3
F
4
4
3
L
4
4
6
M
4
4
7
F
4
5
0
F
4
5
4
A
4
7
9
G
4
8
0
L
4
8
2
L
4
8
3
M
4
8
6
H
5
6
8
E
5
7
1
L
5
7
2
F
5
7
5
[1]3cqv.a fe,hem43 . . . . . * . . . . . . * . . . . . . * . . . .
[1]4n73.a co,coh43 . . . . . M . . . . . . . . . . . . . . . . . .
[2]2v0v.a none - - - - - - . . . . . . . . . . . . . . . . . .
[2]2v7c.b 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
H
3
8
1
L
3
8
2
V
3
8
3
C
3
8
4
P
3
8
5
L
3
8
6
H
3
9
9
W
4
0
2
F
4
0
5
S
4
0
6
F
4
0
9
T
4
1
0
V
4
1
3
F
4
4
3
L
4
4
6
M
4
4
7
F
4
5
0
F
4
5
4
A
4
7
9
G
4
8
0
D
4
8
1
L
4
8
2
L
4
8
3
N
4
8
4
M
4
8
6
H
5
6
8
E
5
7
1
L
5
7
2
L
5
7
3
A
5
7
4
F
5
7
5
[1]3cqv.a . . . . . * . . . . . . . . . * . . . . . . . . * . . . . . .
[1]4n73.a . . . . . M . . . . . . . . . . . . . . . . . . . . . . . . .
[2]2v0v.a - - - - - - . * . . . . . . . . . . . * . * . . * . . * . . .
[2]2v7c.b - - - - - - * * . . * . . . . * . . . * * . * . mse . * . - - -

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
3cqv.a:fe,hem
4n73.a:co,coh
2v0v.a is apo
2v7c.b is apo
[1] 3cqv.a
0.2
0.3 - -
[1] 4n73.a 0.2
0.2
- -
[2] 2v0v.a 14 15
-
-
[2] 2v7c.b 11 12 -
-
[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
3cqv.a
4n73.a
2v0v.a
2v7c.b
[1] 3cqv.a
0
0 .47 .37
[1] 4n73.a 0
0
.47 .38
[2] 2v0v.a .47 .47
0
.22
[2] 2v7c.b .37 .38 .22
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 3.8 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
3cqv.a
4n73.a
2v0v.a
2v7c.b
[1] 3cqv.a
0
0.2 6.7 5.0
[1] 4n73.a 0.2
0
6.8 5.1
[2] 2v0v.a 6.7 6.8
0
1.2
[2] 2v7c.b 5.0 5.1 1.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 3.1 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
3cqv.a
4n73.a
2v0v.a
2v7c.b
[1] 3cqv.a
0
0.4 7.0 6.0
[1] 4n73.a 0.4
0
7.0 6.1
[2] 2v0v.a 7.0 7.0
0
1.6
[2] 2v7c.b 6.0 6.1 1.6
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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