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BRD3_HUMAN_305_416

Bromodomain-containing protein 3

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (BRD3_HUMAN):D: Bromo 2 (332:334, 338, 343:347, 387, 390:392, 394:397)
400
332:334, 338, 343:347, 387, 390:392, 394:397, 400

Full PDB list

2oo1, 3s92, 5a7c, 5hfr, 5hjc

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
W
3
3
2
P
3
3
3
F
3
3
4
V
3
3
8
L
3
4
3
L
3
4
5
D
3
4
7
C
3
8
7
N
3
9
1
P
3
9
2
D
3
9
4
H
3
9
5
E
3
9
6
V
3
9
7
M
4
0
0
[1]2oo1.d none . . . . . . . . . . . . . . .
[1]3s92.a jq131 . . . . . . . . . . . . . . .
[1]5a7c.a 5d414 . . . . . . . . . . . . . . .
[1]5hfr.d none . . . . . . . . . . . R . . .
[1]5hjc.a APRalyQLATK73 . . . . . . . . . . . . . . .

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
3
2
P
3
3
3
F
3
3
4
V
3
3
8
L
3
4
3
E
3
4
4
L
3
4
5
H
3
4
6
D
3
4
7
C
3
8
7
Y
3
9
0
N
3
9
1
P
3
9
2
D
3
9
4
H
3
9
5
E
3
9
6
V
3
9
7
M
4
0
0
[1]2oo1.d . . . . . . . . . . . . . . . . . .
[1]3s92.a . . . . . . . . . . . . . . . . . .
[1]5a7c.a . . . . . . . . . . . . . . . . . .
[1]5hfr.d . . . . . . . . . . . . . . R . . .
[1]5hjc.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
2oo1.d is apo
3s92.a:jq1
5a7c.a:5d4
5hfr.d is apo
5hjc.a:APRalyQLATK
[1] 2oo1.d
-
0.2 0 - 0
[1] 3s92.a -
0
0 - 0.7
[1] 5a7c.a - 0.4
0
- 0.1
[1] 5hfr.d - 0.1 0
-
0.5
[1] 5hjc.a - 0.3 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
2oo1.d
3s92.a
5a7c.a
5hfr.d
5hjc.a
[1] 2oo1.d
0
.04 .01 .03 .01
[1] 3s92.a .04
0
.04 .01 .04
[1] 5a7c.a .01 .04
0
.03 .01
[1] 5hfr.d .03 .01 .03
0
.03
[1] 5hjc.a .01 .04 .01 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
2oo1.d
3s92.a
5a7c.a
5hfr.d
5hjc.a
[1] 2oo1.d
0
0.5 0.2 0.2 0.4
[1] 3s92.a 0.5
0
0.4 0.4 0.5
[1] 5a7c.a 0.2 0.4
0
0.3 0.3
[1] 5hfr.d 0.2 0.4 0.3
0
0.4
[1] 5hjc.a 0.4 0.5 0.3 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
2oo1.d
3s92.a
5a7c.a
5hfr.d
5hjc.a
[1] 2oo1.d
0
1.0 0.5 0.5 0.7
[1] 3s92.a 1.0
0
0.9 0.7 0.9
[1] 5a7c.a 0.5 0.9
0
0.4 0.5
[1] 5hfr.d 0.5 0.7 0.4
0
0.6
[1] 5hjc.a 0.7 0.9 0.5 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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