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ASM3A_MOUSE_22_445

Acid sphingomyelinase-like phosphodiesterase 3a [Acid sphingomyelinase family]

Composition of the binding site

Protein chains monomer
A1 (ASM3A_MOUSE):42, 44, 107, 111, 148, 149, 211, 257, 290, 292, 293, 32442, 44, 107, 111, 148, 149, 211, 257, 290, 292, 293, 324
Metals (Me):Zn

Full PDB list

5fc1, 5fc5, 5fc6, 5fc7, 5fca, 5fcb (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
D
4
2
H
4
4
D
1
0
7
H
1
1
1
N
1
4
8
H
1
4
9
Y
2
1
1
Y
2
5
7
H
2
9
0
H
2
9
2
Q
3
2
4
[1]5fc5.a pc11 . . . . . . . . . . . Zn
[1]5fc6.a ap227 . . . . . . . . . . . Zn
[1]5fc7.a none . . . . . . . . . . . Zn
[1]5fca.b zn1 . . . . . . . . . . . Zn
[1]5fcb.a amp23 . . . . . . . . . . . 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

[download in TSV format]
   
PDB.ch
A1 Me
D
4
2
H
4
4
D
1
0
7
H
1
1
1
N
1
4
8
H
1
4
9
Y
2
1
1
Y
2
5
7
H
2
9
0
H
2
9
2
R
2
9
3
Q
3
2
4
[1]5fc5.a . . . . . . . . . . . . Zn
[1]5fc6.a . . . . . . . . . . . . Zn
[1]5fc7.a . . . . . . . . . . . . Zn
[1]5fca.b . . . . . . . . . . . . Zn
[1]5fcb.a . . . . . . . . . . . . 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
5fc5.a:pc
5fc6.a:ap2
5fc7.a is apo
5fca.b:zn
5fcb.a:amp
[1] 5fc5.a
0
0.1 - 0.1 0.1
[1] 5fc6.a 0
0.1
- 0.1 0.1
[1] 5fc7.a 0 0.1
-
0.1 0.1
[1] 5fca.b 0 0.1 -
0.1
0
[1] 5fcb.a 0 0.1 - 0.1
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
5fc5.a
5fc6.a
5fc7.a
5fca.b
5fcb.a
[1] 5fc5.a
0
0 0 0 0
[1] 5fc6.a 0
0
0 0 0
[1] 5fc7.a 0 0
0
0 0
[1] 5fca.b 0 0 0
0
0
[1] 5fcb.a 0 0 0 0
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
5fc5.a
5fc6.a
5fc7.a
5fca.b
5fcb.a
[1] 5fc5.a
0
0.1 0.2 0.1 0.1
[1] 5fc6.a 0.1
0
0.2 0.1 0.1
[1] 5fc7.a 0.2 0.2
0
0.2 0.2
[1] 5fca.b 0.1 0.1 0.2
0
0.1
[1] 5fcb.a 0.1 0.1 0.2 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
5fc5.a
5fc6.a
5fc7.a
5fca.b
5fcb.a
[1] 5fc5.a
0
0.1 0.3 0.2 0.1
[1] 5fc6.a 0.1
0
0.4 0.2 0.1
[1] 5fc7.a 0.3 0.4
0
0.4 0.4
[1] 5fca.b 0.2 0.2 0.4
0
0.2
[1] 5fcb.a 0.1 0.1 0.4 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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