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LYPL1_HUMAN_1_237

Lysophospholipase-like protein 1 [AB hydrolase superfamily. AB hydrolase 2 family]

Composition of the binding site

Protein chains monomer
A1 (LYPL1_HUMAN):29, 30, 66, 80, 83, 124, 125, 150, 181, 18229, 30, 66, 80, 83, 124, 125, 150, 181, 182

Full PDB list

3u0v, 5kre

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
G
2
9
S
3
0
Y
6
6
R
8
0
I
8
3
S
1
2
4
M
1
2
5
F
1
5
0
L
1
8
1
V
1
8
2
[1]3u0v.a none . . . . . . . . . .
[1]5kre.a 6wg14 . . . . . * . . . .

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
G
2
9
S
3
0
Y
6
6
R
8
0
I
8
3
S
1
2
4
M
1
2
5
F
1
5
0
L
1
8
1
V
1
8
2
[1]3u0v.a . . . . . . . . . .
[1]5kre.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
3u0v.a is apo
5kre.a:6wg
[1] 3u0v.a
-
0.5
[1] 5kre.a -
0.6
[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
3u0v.a
5kre.a
[1] 3u0v.a
0
.03
[1] 5kre.a .03
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
3u0v.a
5kre.a
[1] 3u0v.a
0
0.3
[1] 5kre.a 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

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
3u0v.a
5kre.a
[1] 3u0v.a
0
0.7
[1] 5kre.a 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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