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BRD1_HUMAN_924_1049

Bromodomain-containing protein 1

Composition of the binding site

Protein chains homotrimer [domain annotation]
A1 (BRD1_HUMAN):D: PWWP (937, 940, 943, 991, 993, 997, 999)937, 940, 943, 991, 993, 997, 999
A2 (BRD1_HUMAN):1025, 10261025, 1026
A3 (BRD1_HUMAN):D: PWWP (973)973

Full PDB list

3lyi, 4z02

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 A3
C
9
3
7
Y
9
4
0
Y
9
4
3
F
9
9
1
D
9
9
3
S
9
9
7
Q
9
9
9
N
1
0
2
5
S
1
0
2
6
K
9
7
3
[1]3lyi.a ocs10 . . . . . . . . . .
[1]3lyi.b none . . . . . . . . . .
[1]4z02.a 4k813 . . . . . . . . . .

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 A2 A3
C
9
3
7
Y
9
4
0
Y
9
4
3
F
9
9
1
D
9
9
3
S
9
9
7
Q
9
9
9
N
1
0
2
5
S
1
0
2
6
K
9
7
3
[1]3lyi.a . . . . . . . . . .
[1]3lyi.b . . . . . . . . . .
[1]4z02.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
3lyi.a:ocs
3lyi.b is apo
4z02.a:4k8
[1] 3lyi.a
0
- 0
[1] 3lyi.b 0
-
0
[1] 4z02.a 0.1 -
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
3lyi.a
3lyi.b
4z02.a
[1] 3lyi.a
0
0 .01
[1] 3lyi.b 0
0
.01
[1] 4z02.a .01 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
3lyi.a
3lyi.b
4z02.a
[1] 3lyi.a
0
0.4 0.2
[1] 3lyi.b 0.4
0
0.5
[1] 4z02.a 0.2 0.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
3lyi.a
3lyi.b
4z02.a
[1] 3lyi.a
0
0.7 0.6
[1] 3lyi.b 0.7
0
0.9
[1] 4z02.a 0.6 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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