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ADHX_HUMAN_2_374

Alcohol dehydrogenase class-3 [Zinc-containing alcohol dehydrogenase family. Class-III subfamily]

Composition of the binding site

Protein chains homodimer
A1 (ADHX_HUMAN):45, 47, 56:58, 67, 68, 93, 94, 110, 112, 115, 118, 141, 174, 293:296, 31845, 47, 56:58, 67, 68, 93, 94, 110, 112, 115, 118, 141, 174, 293:296, 318
A2 (ADHX_HUMAN):284, 306, 309, 310284, 306, 309, 310
Cofactors (cF):apr/nad
Metals (Me):Zn

Full PDB list

1m6h, 1m6w, 1ma0, 1mc5, 1mp0, 1teh, 2fze, 2fzw, 3qj5 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 cF Me
C
4
5
T
4
7
D
5
6
P
5
7
E
5
8
H
6
7
E
6
8
Y
9
3
I
9
4
L
1
1
0
Q
1
1
2
R
1
1
5
Q
1
1
8
M
1
4
1
C
1
7
4
G
2
9
3
V
2
9
4
A
3
1
8
K
2
8
4
F
3
0
6
V
3
0
9
T
3
1
0
[1]1m6w.a 12h15 . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1ma0.a dao14 . . . . . . . . . . . . . . . . . . . . . . nad Zn
[1]1ma0.b dao,zn15 . . . . . . . . . . . . . . . . . . . . . . nad Zn
[1]1mc5.a ahe22 . . . . . . . . . . . . . . . . . . . . . . nad Zn
[1]1mc5.b zn1 . . . . . . . . . . . . . . . . . . . . . . nad Zn
[1]2fze.a none . . . . . . . . . . . . . . . . . . . . . . apr Zn
[1]2fzw.a none . . . . . . L . . . . . . . . . . . . . . . nad Zn
[1]3qj5.a 02231 . . . . . . . . . . . . . . . . . . . . . . nad 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

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PDB.ch
A1 A2 cF Me
C
4
5
T
4
7
D
5
6
P
5
7
E
5
8
H
6
7
E
6
8
Y
9
3
I
9
4
L
1
1
0
Q
1
1
2
R
1
1
5
Q
1
1
8
M
1
4
1
C
1
7
4
G
2
9
3
V
2
9
4
A
2
9
5
A
2
9
6
A
3
1
8
K
2
8
4
F
3
0
6
V
3
0
9
T
3
1
0
[1]1m6w.a . * . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1ma0.a . . . . . . . . . . . . . . . . . . . . . . . . nad Zn
[1]1ma0.b . . . . . . . . . . . . . . . . . . . . . . . . nad Zn
[1]1mc5.a . * . . . . . . . . . . . . . . . . . . . . . . nad Zn
[1]1mc5.b . . . . . . . . . . . . . . . . . . . . . . . . nad Zn
[1]2fze.a . . . . . . . . . . . . . . . . . . . . . . . . apr Zn
[1]2fzw.a . . . . . . L . . . . . . . . . . . . . . . . . nad Zn
[1]3qj5.a . . . . . . . . . . . . . . . . . . . . . . . . nad 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
1m6w.a:12h
1ma0.a:dao
1ma0.b:dao,zn
1mc5.a:ahe
1mc5.b:zn
2fze.a is apo
2fzw.a is apo
3qj5.a:022
[1] 1m6w.a
0.2
0.7 1.4 0.1 0.7 - - 1.5
[1] 1ma0.a 0.1
0.3
0.8 0 0.5 - - 0.7
[1] 1ma0.b 0.1 0.4
0.6
0 0.6 - - 0.9
[1] 1mc5.a 0.5 1.0 1.0
0.1
0.7 - - 1.2
[1] 1mc5.b 0.2 0.8 0.4 0
0.4
- - 0.9
[1] 2fze.a 0.3 0.6 0.8 0 0.5
-
- 0.8
[1] 2fzw.a 0.4 0.5 0.8 0 0.5 -
-
1.0
[1] 3qj5.a 0.1 0.3 0.5 0 0.6 - -
0.1
[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
1m6w.a
1ma0.a
1ma0.b
1mc5.a
1mc5.b
2fze.a
2fzw.a
3qj5.a
[1] 1m6w.a
0
.06 .05 .05 .06 .05 .05 .08
[1] 1ma0.a .06
0
.03 .07 .03 .01 .02 .05
[1] 1ma0.b .05 .03
0
.05 .03 .03 .02 .04
[1] 1mc5.a .05 .07 .05
0
.07 .06 .06 .07
[1] 1mc5.b .06 .03 .03 .07
0
.03 .05 .06
[1] 2fze.a .05 .01 .03 .06 .03
0
.01 .05
[1] 2fzw.a .05 .02 .02 .06 .05 .01
0
.04
[1] 3qj5.a .08 .05 .04 .07 .06 .05 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
1m6w.a
1ma0.a
1ma0.b
1mc5.a
1mc5.b
2fze.a
2fzw.a
3qj5.a
[1] 1m6w.a
0
1.8 1.8 1.9 1.9 1.7 1.8 1.7
[1] 1ma0.a 1.8
0
0.3 1.0 0.4 0.3 0.3 0.3
[1] 1ma0.b 1.8 0.3
0
0.9 0.3 0.2 0.3 0.3
[1] 1mc5.a 1.9 1.0 0.9
0
1.0 0.9 1.0 1.0
[1] 1mc5.b 1.9 0.4 0.3 1.0
0
0.4 0.4 0.5
[1] 2fze.a 1.7 0.3 0.2 0.9 0.4
0
0.3 0.2
[1] 2fzw.a 1.8 0.3 0.3 1.0 0.4 0.3
0
0.4
[1] 3qj5.a 1.7 0.3 0.3 1.0 0.5 0.2 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
1m6w.a
1ma0.a
1ma0.b
1mc5.a
1mc5.b
2fze.a
2fzw.a
3qj5.a
[1] 1m6w.a
0
2.0 2.1 2.0 2.0 2.0 2.1 2.1
[1] 1ma0.a 2.0
0
1.0 1.4 0.8 0.9 1.0 1.0
[1] 1ma0.b 2.1 1.0
0
1.4 0.9 0.5 0.5 0.6
[1] 1mc5.a 2.0 1.4 1.4
0
1.3 1.4 1.5 1.5
[1] 1mc5.b 2.0 0.8 0.9 1.3
0
1.0 1.0 1.1
[1] 2fze.a 2.0 0.9 0.5 1.4 1.0
0
0.6 0.6
[1] 2fzw.a 2.1 1.0 0.5 1.5 1.0 0.6
0
0.6
[1] 3qj5.a 2.1 1.0 0.6 1.5 1.1 0.6 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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