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CRBN_CHICK_320_432

Protein cereblon [CRBN family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CRBN_CHICK):D: CULT (353:355, 359, 379:382, 388, 402, 404)
R: Thalidomide binding (380:382, 388)
353:355, 359, 379:382, 388, 402, 404
Metals (Me):Zn

Full PDB list

4ci1, 4ci2, 4ci3

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
N
3
5
3
P
3
5
4
H
3
5
5
H
3
5
9
E
3
7
9
H
3
8
0
S
3
8
1
W
3
8
2
W
3
8
8
W
4
0
2
F
4
0
4
[1]4ci1.b ef219 . . . . . . . . . . . Zn
[1]4ci2.b lvy19 . . . . . . . . . . . Zn
[1]4ci3.b y7020 . . . . . . . . . . . Zn

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 Me
N
3
5
3
P
3
5
4
H
3
5
5
H
3
5
9
E
3
7
9
H
3
8
0
S
3
8
1
W
3
8
2
W
3
8
8
W
4
0
2
F
4
0
4
[1]4ci1.b . . . . . . . . . . . Zn
[1]4ci2.b . . . . . . . . . . . Zn
[1]4ci3.b . . . . . . . . . . . Zn

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
4ci1.b:ef2
4ci2.b:lvy
4ci3.b:y70
[1] 4ci1.b
0
0 0
[1] 4ci2.b 0
0
0
[1] 4ci3.b 0 0
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
4ci1.b
4ci2.b
4ci3.b
[1] 4ci1.b
0
0 0
[1] 4ci2.b 0
0
0
[1] 4ci3.b 0 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.1 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
4ci1.b
4ci2.b
4ci3.b
[1] 4ci1.b
0
0.1 0.1
[1] 4ci2.b 0.1
0
0.2
[1] 4ci3.b 0.1 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
4ci1.b
4ci2.b
4ci3.b
[1] 4ci1.b
0
0.6 0.1
[1] 4ci2.b 0.6
0
0.6
[1] 4ci3.b 0.1 0.6
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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