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ASM_MOUSE_164_614

Sphingomyelin phosphodiesterase [Acid sphingomyelinase family]

Composition of the binding site

Protein chains monomer
A1 (ASM_MOUSE):204, 206, 276, 280, 316, 317, 455:458, 486, 487, 489, 573204, 206, 276, 280, 316, 317, 455:458, 486, 487, 489, 573
Metals (Me):Zn

Full PDB list

5fi9, 5fib, 5fic, 5hqn (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 Me
D
2
0
4
H
2
0
6
D
2
7
6
H
2
8
0
N
3
1
6
H
3
1
7
H
4
5
5
T
4
5
6
H
4
5
7
V
4
5
8
I
4
8
7
H
5
7
3
[1]5fi9.a nt819 . . . . . . . . . . . . Zn
[1]5fic.c none . . . . . . . . . . . . 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 Me
D
2
0
4
H
2
0
6
D
2
7
6
H
2
8
0
N
3
1
6
H
3
1
7
H
4
5
5
T
4
5
6
H
4
5
7
V
4
5
8
F
4
8
6
I
4
8
7
L
4
8
9
H
5
7
3
[1]5fi9.a . . . . . . . . . . . . . . Zn
[1]5fic.c . . . . . . . . . . . . . . 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
5fi9.a:nt8
5fic.c is apo
[1] 5fi9.a
0
-
[1] 5fic.c 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
5fi9.a
5fic.c
[1] 5fi9.a
0
.01
[1] 5fic.c .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
5fi9.a
5fic.c
[1] 5fi9.a
0
0.3
[1] 5fic.c 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
5fi9.a
5fic.c
[1] 5fi9.a
0
0.5
[1] 5fic.c 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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