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NR4A1_HUMAN_350_598

Nuclear receptor subfamily 4 group A member 1 [Nuclear hormone receptor family. NR4 subfamily]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (NR4A1_HUMAN):D: NR LBD (437, 440:445, 510, 513:515, 562:564, 566, 567, 570, 591, 592, 594, 595)
596, 597
437, 440:445, 510, 513:515, 562:564, 566, 567, 570, 591, 592, 594:597
A2 (NR4A1_HUMAN):D: NR LBD (578)578

Full PDB list

1yje, 2qw4, 3v3e, 3v3q, 4jgv, 4kzi, 4kzj, 4kzm, 4re8, 4ree, 4ref, 4rze, 4rzf, 4rzg, 4whf, 4whg (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
L
4
3
7
E
4
4
0
S
4
4
1
A
4
4
2
F
4
4
3
L
4
4
4
E
4
4
5
V
5
1
0
T
5
1
3
D
5
1
4
R
5
1
5
R
5
6
3
C
5
6
6
T
5
6
7
L
5
7
0
I
5
9
1
F
5
9
2
D
5
9
4
T
5
9
5
[1]3v3q.a tmy27 . . . . . . . . . . . . . . . . . . .
[1]4kzi.a zj021 . . . . . . . . . . . . . . . . . . .
[1]4ree.a none . . . . . . . . . . . . . . . . . . .
[1]4rzg.a zhn27 . . . . . . . . . . . . . . . . . . .
[2]3v3e.b none . . . . . . . . . . . . . . . . . . .
[2]4rze.b none W . . . . . . . . . . . . . . . . E .
[3]4rzf.b none . . W . . . . . . . . . . . . . . . .

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

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PDB.ch
A1 A2
L
4
3
7
E
4
4
0
S
4
4
1
A
4
4
2
F
4
4
3
L
4
4
4
E
4
4
5
V
5
1
0
T
5
1
3
D
5
1
4
R
5
1
5
L
5
6
2
R
5
6
3
T
5
6
4
C
5
6
6
T
5
6
7
L
5
7
0
I
5
9
1
F
5
9
2
D
5
9
4
T
5
9
5
L
5
9
6
P
5
9
7
L
5
7
8
[1]3v3q.a . . . . . . . . . . . . . . . . . . . . . . . .
[1]4kzi.a . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ree.a . . . . . . * . . . . . . . . . . . . . . . . .
[1]4rzg.a . . . . . . * . . . . . . . . . . . . . . . . .
[2]3v3e.b . . . . . . * . . . . . * . * . . . . . * . . .
[2]4rze.b W . . . . . * . . . . . * . * . . . . E * . . .
[3]4rzf.b . . W . . . * . . . . . * . * . . . . . * . * .

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
3v3q.a:tmy
4kzi.a:zj0
4ree.a is apo
4rzg.a:zhn
3v3e.b is apo
4rze.b is apo
4rzf.b is apo
[1] 3v3q.a
0.7
0.7 - 0.3 - - -
[1] 4kzi.a 1.0
0.5
- 0.2 - - -
[1] 4ree.a 1.2 1.3
-
0.5 - - -
[1] 4rzg.a 1.3 1.1 -
0.1
- - -
[2] 3v3e.b 4.2 6.0 - 2.3
-
- -
[2] 4rze.b 5.0 5.9 - 5.2 -
-
-
[3] 4rzf.b 6.4 5.3 - 7.5 - -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (3 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
3v3q.a
4kzi.a
4ree.a
4rzg.a
3v3e.b
4rze.b
4rzf.b
[1] 3v3q.a
0
.02 .05 .03 .30 .43 .50
[1] 4kzi.a .02
0
.05 .03 .29 .42 .49
[1] 4ree.a .05 .05
0
.05 .25 .38 .45
[1] 4rzg.a .03 .03 .05
0
.28 .40 .47
[2] 3v3e.b .30 .29 .25 .28
0
.14 .30
[2] 4rze.b .43 .42 .38 .40 .14
0
.41
[3] 4rzf.b .50 .49 .45 .47 .30 .41
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
3v3q.a
4kzi.a
4ree.a
4rzg.a
3v3e.b
4rze.b
4rzf.b
[1] 3v3q.a
0
0.2 0.4 0.2 1.1 1.2 1.2
[1] 4kzi.a 0.2
0
0.3 0.2 1.0 1.1 1.2
[1] 4ree.a 0.4 0.3
0
0.3 0.9 1.0 1.1
[1] 4rzg.a 0.2 0.2 0.3
0
1.0 1.1 1.2
[2] 3v3e.b 1.1 1.0 0.9 1.0
0
0.3 0.4
[2] 4rze.b 1.2 1.1 1.0 1.1 0.3
0
0.4
[3] 4rzf.b 1.2 1.2 1.1 1.2 0.4 0.4
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
3v3q.a
4kzi.a
4ree.a
4rzg.a
3v3e.b
4rze.b
4rzf.b
[1] 3v3q.a
0
0.6 0.7 0.8 1.7 1.8 1.8
[1] 4kzi.a 0.6
0
0.4 0.3 1.4 1.6 1.5
[1] 4ree.a 0.7 0.4
0
0.5 1.3 1.5 1.4
[1] 4rzg.a 0.8 0.3 0.5
0
1.4 1.5 1.5
[2] 3v3e.b 1.7 1.4 1.3 1.4
0
0.6 0.5
[2] 4rze.b 1.8 1.6 1.5 1.5 0.6
0
0.7
[3] 4rzf.b 1.8 1.5 1.4 1.5 0.5 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

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