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ASM_HUMAN_46_629

Sphingomyelin phosphodiesterase [Acid sphingomyelinase family]

Composition of the binding site

Protein chains monomer
A1 (ASM_HUMAN):208, 278, 282, 318, 319, 457, 459, 488208, 278, 282, 318, 319, 457, 459, 488
Metals (Me):Zn

Full PDB list

5i81, 5i85, 5jg8 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
H
2
0
8
D
2
7
8
H
2
8
2
N
3
1
8
H
3
1
9
H
4
5
7
H
4
5
9
Y
4
8
8
[1]5i81.a none . . . . . . . . Zn
[1]5i85.a pc11 . . . . . . . . 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
H
2
0
8
D
2
7
8
H
2
8
2
N
3
1
8
H
3
1
9
H
4
5
7
H
4
5
9
Y
4
8
8
[1]5i81.a . . . . . . . . Zn
[1]5i85.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
5i81.a is apo
5i85.a:pc
[1] 5i81.a
-
0.1
[1] 5i85.a -
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
5i81.a
5i85.a
[1] 5i81.a
0
.01
[1] 5i85.a .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
5i81.a
5i85.a
[1] 5i81.a
0
0.1
[1] 5i85.a 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
5i81.a
5i85.a
[1] 5i81.a
0
0.7
[1] 5i85.a 0.7
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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