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NNMT_MOUSE_2_264

Nicotinamide N-methyltransferase [Class I-like SAM-binding methyltransferase superfamily. NNMT/PNMT/TEMT family]

Composition of the binding site

Protein chains monomer
A1 (NNMT_MOUSE):20, 24, 164, 167, 198, 201, 204, 213, 242, 24720, 24, 164, 167, 198, 201, 204, 213, 242, 247
Cofactors (cF):sah

Full PDB list

2i62, 5xvk, 5yji

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
Y
2
0
Y
2
4
L
1
6
4
D
1
6
7
A
1
9
8
S
2
0
1
Y
2
0
4
S
2
1
3
Y
2
4
2
[1]2i62.b none . . . . . . . . .
[1]5xvk.a 8gc10 . . . . . . . . . sah
[1]5yji.a 8wo12 . . . . . . . . . sah

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 cF
Y
2
0
Y
2
4
L
1
6
4
D
1
6
7
A
1
9
8
S
2
0
1
Y
2
0
4
S
2
1
3
Y
2
4
2
S
2
4
7
[1]2i62.b . . . . . . . . . .
[1]5xvk.a . . . . . . . . . . sah
[1]5yji.a . . . . . . . . . . sah

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
2i62.b is apo
5xvk.a:8gc
5yji.a:8wo
[1] 2i62.b
-
0.1 0.3
[1] 5xvk.a -
0
0.1
[1] 5yji.a - 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
2i62.b
5xvk.a
5yji.a
[1] 2i62.b
0
.02 .03
[1] 5xvk.a .02
0
.01
[1] 5yji.a .03 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.2 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
2i62.b
5xvk.a
5yji.a
[1] 2i62.b
0
0.3 0.4
[1] 5xvk.a 0.3
0
0.1
[1] 5yji.a 0.4 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
2i62.b
5xvk.a
5yji.a
[1] 2i62.b
0
0.3 0.4
[1] 5xvk.a 0.3
0
0.2
[1] 5yji.a 0.4 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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