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HSAD_MYCTU_3_290

4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase [AB hydrolase superfamily. HsaD family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (HSAD_MYCTU):R: Substrate binding (45, 46)
44, 49, 54, 113:115, 140, 154, 155, 158, 173, 177, 192, 208, 209, 212, 243, 244, 269, 270
44:46, 49, 54, 113:115, 140, 154, 155, 158, 173, 177, 192, 208, 209, 212, 243, 244, 269, 270

Full PDB list

2vf2, 2wud, 2wue, 2wuf, 2wug, 5jz9, 5jzb, 5jzs (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
G
4
4
G
4
5
G
4
6
A
4
9
N
5
4
N
1
1
3
S
1
1
4
L
1
1
5
G
1
4
0
G
1
5
4
V
1
5
5
L
1
5
8
F
1
7
3
M
1
7
7
R
1
9
2
M
2
0
8
F
2
1
2
V
2
4
3
N
2
4
4
H
2
6
9
W
2
7
0
[1]2wue.b kek20 . . . . . . A . . . . . . . . . . . . . .
[1]2wuf.a none . . . . . . A . . . . . . . . . . . . . .
[1]2wuf.b kem25 . . . . . . A . . . . . . . . . . . . . .
[1]2wug.a hpk16 . . . . . . A . . . . . . . . . . . . . .
[1]5jz9.b 6or13 . . . . . . . . . . . . . . . . . . . . .
[1]5jzb.b 6ot12 . . . . . . . . . . . . . . . . . . . . .
[1]5jzs.a none . . . . . . . . . . . . . . . . . . . . .
[1]5jzs.b fgz12 . . . . . . . . . . . . . . . . . . . . .

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
G
4
4
G
4
5
G
4
6
A
4
9
N
5
4
N
1
1
3
S
1
1
4
L
1
1
5
G
1
4
0
G
1
5
4
V
1
5
5
L
1
5
8
F
1
7
3
M
1
7
7
R
1
9
2
M
2
0
8
G
2
0
9
F
2
1
2
V
2
4
3
N
2
4
4
H
2
6
9
W
2
7
0
[1]2wue.b . . . . . . A . . . . . . . . . . . . . . .
[1]2wuf.a . . . . . . A . . . . . . . . * . . . . . .
[1]2wuf.b . . . . . . A . . . . . . . . * . . . . . .
[1]2wug.a . . . . . . A . . . . . . . . . . . . . . .
[1]5jz9.b . . . . . . . . . . . . . . . . . . . . . .
[1]5jzb.b . * . . . . . . . . . . . . . . . . . . . .
[1]5jzs.a . . . . . . . . . . . . . . . . . . . . . .
[1]5jzs.b . . . . . . . . . . . . . . . . . . . . . .

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
2wue.b:kek
2wuf.a is apo
2wuf.b:kem
2wug.a:hpk
5jz9.b:6or
5jzb.b:6ot
5jzs.a is apo
5jzs.b:fgz
[1] 2wue.b
0.2
- 0 0 0.1 0.4 - 0.2
[1] 2wuf.a 0.2
-
0 0 0.1 0.6 - 0.3
[1] 2wuf.b 0.2 -
0
0 0.1 0.6 - 0.1
[1] 2wug.a 0.2 - 0.1
0
0.4 0.4 - 0.1
[1] 5jz9.b 0.2 - 0.6 0.1
0.1
0 - 0.3
[1] 5jzb.b 1.1 - 0.7 0.5 1.2
0
- 0.6
[1] 5jzs.a 0.1 - 0 0.1 0.2 0
-
0.2
[1] 5jzs.b 0.3 - 0.4 0.1 0.2 0 -
0.3
[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
2wue.b
2wuf.a
2wuf.b
2wug.a
5jz9.b
5jzb.b
5jzs.a
5jzs.b
[1] 2wue.b
0
.02 .01 .03 .05 .10 .04 .05
[1] 2wuf.a .02
0
0 .03 .06 .11 .05 .07
[1] 2wuf.b .01 0
0
.03 .06 .11 .04 .07
[1] 2wug.a .03 .03 .03
0
.06 .09 .04 .06
[1] 5jz9.b .05 .06 .06 .06
0
.08 .03 .01
[1] 5jzb.b .10 .11 .11 .09 .08
0
.08 .08
[1] 5jzs.a .04 .05 .04 .04 .03 .08
0
.03
[1] 5jzs.b .05 .07 .07 .06 .01 .08 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.1 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
2wue.b
2wuf.a
2wuf.b
2wug.a
5jz9.b
5jzb.b
5jzs.a
5jzs.b
[1] 2wue.b
0
0.3 0.1 0.3 0.8 1.0 1.1 0.9
[1] 2wuf.a 0.3
0
0.2 0.3 0.8 1.0 1.1 0.8
[1] 2wuf.b 0.1 0.2
0
0.3 0.8 1.0 1.1 0.8
[1] 2wug.a 0.3 0.3 0.3
0
0.9 1.1 1.2 0.9
[1] 5jz9.b 0.8 0.8 0.8 0.9
0
0.5 0.5 0.2
[1] 5jzb.b 1.0 1.0 1.0 1.1 0.5
0
0.6 0.5
[1] 5jzs.a 1.1 1.1 1.1 1.2 0.5 0.6
0
0.5
[1] 5jzs.b 0.9 0.8 0.8 0.9 0.2 0.5 0.5
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

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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
2wue.b
2wuf.a
2wuf.b
2wug.a
5jz9.b
5jzb.b
5jzs.a
5jzs.b
[1] 2wue.b
0
0.5 0.4 0.7 1.3 1.6 1.4 1.4
[1] 2wuf.a 0.5
0
0.3 0.6 1.2 1.6 1.3 1.3
[1] 2wuf.b 0.4 0.3
0
0.6 1.3 1.6 1.4 1.3
[1] 2wug.a 0.7 0.6 0.6
0
1.2 1.6 1.5 1.2
[1] 5jz9.b 1.3 1.2 1.3 1.2
0
1.1 0.7 0.4
[1] 5jzb.b 1.6 1.6 1.6 1.6 1.1
0
1.1 1.0
[1] 5jzs.a 1.4 1.3 1.4 1.5 0.7 1.1
0
0.7
[1] 5jzs.b 1.4 1.3 1.3 1.2 0.4 1.0 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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