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BPHL_HUMAN_38_291

Valacyclovir hydrolase [AB hydrolase superfamily. Lipase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (BPHL_HUMAN):D: AB hydrolase-1 (68, 69, 139, 140, 172, 175, 176, 179)
209, 246, 247, 272
68, 69, 139, 140, 172, 175, 176, 179, 209, 246, 247, 272
Metals (Me):Mg/Mn

Full PDB list

2ocg, 2oci, 2ock, 2ocl

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
G
6
8
M
6
9
S
1
3
9
D
1
4
0
I
1
7
5
Y
1
7
6
I
1
7
9
W
2
0
9
V
2
4
7
H
2
7
2
[1]2ocg.a none . . . . . . . . . . Mg,Mn
[1]2oci.a tyc13 . . . . . . . . . . Mg,Mn
[1]2ock.a none . . . N . . . . . . Mg,Mn
[1]2ocl.a none . . A . . . . . . . Mg,Mn

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
G
6
8
M
6
9
S
1
3
9
D
1
4
0
D
1
7
2
I
1
7
5
Y
1
7
6
I
1
7
9
W
2
0
9
L
2
4
6
V
2
4
7
H
2
7
2
[1]2ocg.a . . . . . . . . . . . . Mg,Mn
[1]2oci.a . . . . . . . . . . . . Mg,Mn
[1]2ock.a . . . N . . * . . . . . Mg,Mn
[1]2ocl.a . . A . . . . . . . . . Mg,Mn

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
2ocg.a is apo
2oci.a:tyc
2ock.a is apo
2ocl.a is apo
[1] 2ocg.a
-
1.3 - -
[1] 2oci.a -
0
- -
[1] 2ock.a - 1.8
-
-
[1] 2ocl.a - 1.0 -
-
[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
2ocg.a
2oci.a
2ock.a
2ocl.a
[1] 2ocg.a
0
.11 .09 .03
[1] 2oci.a .11
0
.15 .08
[1] 2ock.a .09 .15
0
.10
[1] 2ocl.a .03 .08 .10
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
2ocg.a
2oci.a
2ock.a
2ocl.a
[1] 2ocg.a
0
0.4 0.4 0.2
[1] 2oci.a 0.4
0
0.6 0.5
[1] 2ock.a 0.4 0.6
0
0.3
[1] 2ocl.a 0.2 0.5 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
2ocg.a
2oci.a
2ock.a
2ocl.a
[1] 2ocg.a
0
1.3 0.5 0.4
[1] 2oci.a 1.3
0
1.5 1.4
[1] 2ock.a 0.5 1.5
0
0.4
[1] 2ocl.a 0.4 1.4 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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