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NNMT_HUMAN_1_264

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (NNMT_HUMAN):R: S-adenosyl-L-methionine binding (63, 64)
R: S-adenosyl-L-methionine binding (142, 143)
11, 15, 20, 24, 25, 65, 67, 69, 70, 85:87, 90, 141, 144, 163:165, 167:169, 197, 198, 201, 203, 204, 213, 242
11, 15, 20, 24, 25, 63:65, 67, 69, 70, 85:87, 90, 141:144, 163:165, 167:169, 197, 198, 201, 203, 204, 213, 242

Full PDB list

2iip, 3rod, 5xvq, 5yjf, 6b1a

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
1
1
F
1
5
Y
2
0
Y
2
4
Y
2
5
G
6
3
S
6
4
G
6
5
T
6
7
Y
6
9
Q
7
0
D
8
5
Y
8
6
S
8
7
N
9
0
C
1
4
1
D
1
4
2
V
1
4
3
T
1
4
4
T
1
6
3
L
1
6
4
C
1
6
5
D
1
6
7
A
1
6
8
A
1
6
9
D
1
9
7
A
1
9
8
S
2
0
1
Y
2
0
4
S
2
1
3
Y
2
4
2
[1]2iip.a sah26 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3rod.a nca,sah35 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5xvq.b 8gc,sah36 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5yjf.a 8wo,sah38 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]6b1a.a c8j38 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
Y
1
1
F
1
5
Y
2
0
Y
2
4
Y
2
5
G
6
3
S
6
4
G
6
5
T
6
7
Y
6
9
Q
7
0
D
8
5
Y
8
6
S
8
7
N
9
0
C
1
4
1
D
1
4
2
V
1
4
3
T
1
4
4
T
1
6
3
L
1
6
4
C
1
6
5
D
1
6
7
A
1
6
8
A
1
6
9
D
1
9
7
A
1
9
8
S
2
0
1
Y
2
0
3
Y
2
0
4
S
2
1
3
Y
2
4
2
[1]2iip.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3rod.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5xvq.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5yjf.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]6b1a.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
2iip.a:sah
3rod.a:nca,sah
5xvq.b:8gc,sah
5yjf.a:8wo,sah
6b1a.a:c8j
[1] 2iip.a
0
0.5 0.1 0.6 0.2
[1] 3rod.a 0
0.2
0.1 0.5 0.4
[1] 5xvq.b 0.1 0.3
0.1
0.5 0.2
[1] 5yjf.a 0.2 0.3 0.2
0.2
0.2
[1] 6b1a.a 0.3 0.3 0.5 0.4
0.2
[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
2iip.a
3rod.a
5xvq.b
5yjf.a
6b1a.a
[1] 2iip.a
0
.01 .02 .02 .02
[1] 3rod.a .01
0
.02 .02 .02
[1] 5xvq.b .02 .02
0
.02 .03
[1] 5yjf.a .02 .02 .02
0
.02
[1] 6b1a.a .02 .02 .03 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
2iip.a
3rod.a
5xvq.b
5yjf.a
6b1a.a
[1] 2iip.a
0
0.3 0.3 0.3 0.2
[1] 3rod.a 0.3
0
0.3 0.3 0.3
[1] 5xvq.b 0.3 0.3
0
0.3 0.3
[1] 5yjf.a 0.3 0.3 0.3
0
0.3
[1] 6b1a.a 0.2 0.3 0.3 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
2iip.a
3rod.a
5xvq.b
5yjf.a
6b1a.a
[1] 2iip.a
0
0.4 0.8 0.5 0.7
[1] 3rod.a 0.4
0
0.7 0.5 0.8
[1] 5xvq.b 0.8 0.7
0
0.8 0.6
[1] 5yjf.a 0.5 0.5 0.8
0
0.8
[1] 6b1a.a 0.7 0.8 0.6 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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