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HNMT_HUMAN_1_292

Histamine N-methyltransferase [Class I-like SAM-binding methyltransferase superfamily. HNMT family]

Composition of the binding site

Protein chains monomer
A1 (HNMT_HUMAN):7:9, 15, 16, 19, 22, 23, 28, 29, 32, 59:63, 65, 66, 88:91, 94, 119, 120, 142:144, 146, 147, 173, 179, 183, 193:198, 243, 246, 283, 2857:9, 15, 16, 19, 22, 23, 28, 29, 32, 59:63, 65, 66, 88:91, 94, 119, 120, 142:144, 146, 147, 173, 179, 183, 193:198, 243, 246, 283, 285

Full PDB list

1jqd, 1jqe, 2aot, 2aou, 2aov, 2aow, 2aox (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
9
Y
1
5
V
1
6
F
1
9
F
2
2
E
2
8
H
2
9
I
5
9
G
6
0
G
6
1
G
6
2
I
6
6
E
8
9
P
9
0
S
9
1
Q
9
4
T
1
1
9
S
1
2
0
I
1
4
2
Q
1
4
3
M
1
4
4
Y
1
4
6
Y
1
4
7
V
1
7
3
W
1
7
9
W
1
8
3
D
1
9
3
L
1
9
5
C
1
9
6
Q
1
9
7
Y
1
9
8
F
2
4
3
E
2
4
6
N
2
8
3
[1]1jqd.a hsm,sah34 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1jqe.a qun,sah54 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1jqe.b sah26 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2aot.b 2pm,sah45 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2aou.b cqa23 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2aov.a 4di,c2m28 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2aow.a tha15 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
S
7
L
8
F
9
Y
1
5
V
1
6
F
1
9
F
2
2
L
2
3
E
2
8
H
2
9
M
3
2
I
5
9
G
6
0
G
6
1
G
6
2
A
6
3
E
6
5
I
6
6
V
8
8
E
8
9
P
9
0
S
9
1
Q
9
4
T
1
1
9
S
1
2
0
I
1
4
2
Q
1
4
3
M
1
4
4
Y
1
4
6
Y
1
4
7
V
1
7
3
W
1
7
9
W
1
8
3
D
1
9
3
D
1
9
4
L
1
9
5
C
1
9
6
Q
1
9
7
Y
1
9
8
F
2
4
3
E
2
4
6
N
2
8
3
L
2
8
5
[1]1jqd.a . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . .
[1]1jqe.a - - - . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . .
[1]1jqe.b - - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . .
[1]2aot.b . . * * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . .
[1]2aou.b . . * * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2aov.a . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . .
[1]2aow.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
1jqd.a:hsm,sah
1jqe.a:qun,sah
1jqe.b:sah
2aot.b:2pm,sah
2aou.b:cqa
2aov.a:4di,c2m
2aow.a:tha
[1] 1jqd.a
0.1
3.4 0.3 0.7 2.2 0.3 0.2
[1] 1jqe.a 0.7
0.1
0.5 1.9 2.1 2.7 1.0
[1] 1jqe.b 0.5 0.6
0.1
2.0 0.7 1.3 0
[1] 2aot.b 0.4 5.2 0.5
0.1
1.9 0.7 0.3
[1] 2aou.b 0.7 4.9 0.5 2.9
0.1
2.5 0.1
[1] 2aov.a 0.1 3.7 0.1 0.6 1.6
0.1
0.1
[1] 2aow.a 1.0 3.6 0.7 2.5 1.9 1.1
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
1jqd.a
1jqe.a
1jqe.b
2aot.b
2aou.b
2aov.a
2aow.a
[1] 1jqd.a
0
.20 .13 .13 .17 .08 .09
[1] 1jqe.a .20
0
.10 .23 .19 .15 .17
[1] 1jqe.b .13 .10
0
.19 .16 .10 .11
[1] 2aot.b .13 .23 .19
0
.20 .14 .16
[1] 2aou.b .17 .19 .16 .20
0
.17 .16
[1] 2aov.a .08 .15 .10 .14 .17
0
.06
[1] 2aow.a .09 .17 .11 .16 .16 .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.3 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
1jqd.a
1jqe.a
1jqe.b
2aot.b
2aou.b
2aov.a
2aow.a
[1] 1jqd.a
0
1.5 1.3 0.5 1.6 0.7 1.3
[1] 1jqe.a 1.5
0
0.9 1.6 0.9 1.3 1.6
[1] 1jqe.b 1.3 0.9
0
1.5 1.1 1.1 1.3
[1] 2aot.b 0.5 1.6 1.5
0
1.6 0.9 1.5
[1] 2aou.b 1.6 0.9 1.1 1.6
0
1.3 1.5
[1] 2aov.a 0.7 1.3 1.1 0.9 1.3
0
1.1
[1] 2aow.a 1.3 1.6 1.3 1.5 1.5 1.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.3 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
1jqd.a
1jqe.a
1jqe.b
2aot.b
2aou.b
2aov.a
2aow.a
[1] 1jqd.a
0
1.8 1.3 0.8 1.8 0.8 1.4
[1] 1jqe.a 1.8
0
0.9 1.7 1.2 1.6 1.7
[1] 1jqe.b 1.3 0.9
0
1.3 1.3 1.2 1.3
[1] 2aot.b 0.8 1.7 1.3
0
1.7 1.1 1.5
[1] 2aou.b 1.8 1.2 1.3 1.7
0
1.5 1.6
[1] 2aov.a 0.8 1.6 1.2 1.1 1.5
0
1.2
[1] 2aow.a 1.4 1.7 1.3 1.5 1.6 1.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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