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BRDT_HUMAN_19_137

Bromodomain testis-specific protein

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (BRDT_HUMAN):D: Bromo 1 (50:52, 56, 57, 61:70, 72, 105, 108, 109, 114, 115)
118
50:52, 56, 57, 61:70, 72, 105, 108, 109, 114, 115, 118

Full PDB list

2rfj, 4flp, 4kcx

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
W
5
0
P
5
1
F
5
2
V
5
6
L
6
1
L
6
3
Y
1
0
8
N
1
0
9
D
1
1
4
I
1
1
5
M
1
1
8
[1]4flp.a jq131 . . . . . . . . . . .
[1]4kcx.a 1qk29 . . . . . . . . . . .
[2]2rfj.a 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

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PDB.ch
A1
W
5
0
P
5
1
F
5
2
V
5
6
D
5
7
L
6
1
Q
6
2
L
6
3
P
6
4
D
6
5
Y
6
6
Y
6
7
T
6
8
I
6
9
I
7
0
N
7
2
C
1
0
5
Y
1
0
8
N
1
0
9
D
1
1
4
I
1
1
5
M
1
1
8
[1]4flp.a . . . . . . . . . . . . . . . . . . . . . .
[1]4kcx.a . . . . . . . . . . . . . . . . . . . . . .
[2]2rfj.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
4flp.a:jq1
4kcx.a:1qk
2rfj.a is apo
[1] 4flp.a
0
1.2 -
[1] 4kcx.a 0.2
0
-
[2] 2rfj.a 11 7.5
-
[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
4flp.a
4kcx.a
2rfj.a
[1] 4flp.a
0
.05 .60
[1] 4kcx.a .05
0
.66
[2] 2rfj.a .60 .66
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.5 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
4flp.a
4kcx.a
2rfj.a
[1] 4flp.a
0
0.7 7.9
[1] 4kcx.a 0.7
0
7.6
[2] 2rfj.a 7.9 7.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 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
4flp.a
4kcx.a
2rfj.a
[1] 4flp.a
0
1.5 8.0
[1] 4kcx.a 1.5
0
8.0
[2] 2rfj.a 8.0 8.0
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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