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BACE2_HUMAN_76_460

Beta-secretase 2 [Peptidase A1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (BACE2_HUMAN):D: Peptidase A1 (92, 108, 110, 112, 113, 148:152, 185, 186, 188, 190, 193, 196, 232, 273, 299, 301, 303:307, 310, 403, 404, 406, 409, 413)
87:91
87:92, 108, 110, 112, 113, 148:152, 185, 186, 188, 190, 193, 196, 232, 273, 299, 301, 303:307, 310, 403, 404, 406, 409, 413

Full PDB list

2ewy, 3zkg, 3zki, 3zkm, 3zkn, 3zkq, 3zks, 3zkx, 3zl7, 3zlq, 4bel, 4bfb (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
D
8
7
S
8
8
G
8
9
R
9
0
G
9
1
Y
9
2
L
1
0
8
D
1
1
0
G
1
1
2
S
1
1
3
K
1
4
8
Y
1
4
9
T
1
5
0
Q
1
5
1
N
1
8
5
F
1
8
6
L
1
8
8
W
1
9
3
I
1
9
6
Y
2
7
3
I
3
0
1
D
3
0
3
S
3
0
4
G
3
0
5
T
3
0
6
T
3
0
7
R
3
1
0
V
4
0
6
A
4
0
9
[1]2ewy.a dbo38 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3zkm.b none . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3zkn.b wzv31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3zl7.a R11 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3zlq.b 6t929 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bel.a b3p19 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
D
8
7
S
8
8
G
8
9
R
9
0
G
9
1
Y
9
2
L
1
0
8
D
1
1
0
G
1
1
2
S
1
1
3
K
1
4
8
Y
1
4
9
T
1
5
0
Q
1
5
1
G
1
5
2
N
1
8
5
F
1
8
6
L
1
8
8
G
1
9
0
W
1
9
3
I
1
9
6
M
2
3
2
Y
2
7
3
K
2
9
9
I
3
0
1
D
3
0
3
S
3
0
4
G
3
0
5
T
3
0
6
T
3
0
7
R
3
1
0
N
4
0
3
A
4
0
4
V
4
0
6
A
4
0
9
E
4
1
3
[1]2ewy.a . . . * . . . . . . . * * * . . . . . . . . . . . . . . . . . . . . . .
[1]3zkm.b . . . . . . . . . . . * . * . . . . . . . . . . . . . . . . . . . . . .
[1]3zkn.b . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3zl7.a . . . . . . . . . . . * . * . . . . . . . . . . . . . . . . . . . . . .
[1]3zlq.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bel.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
2ewy.a:dbo
3zkm.b is apo
3zkn.b:wzv
3zl7.a:R
3zlq.b:6t9
4bel.a:b3p
[1] 2ewy.a
0
- 3.7 1.5 2.7 0.9
[1] 3zkm.b 0.3
-
3.4 1.0 3.8 0.7
[1] 3zkn.b 0.4 -
0
2.7 1.0 0
[1] 3zl7.a 0.7 - 5.8
0
3.4 0.7
[1] 3zlq.b 0.3 - 0.6 0
0.1
0.1
[1] 4bel.a 0.3 - 3.5 0.1 2.8
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
2ewy.a
3zkm.b
3zkn.b
3zl7.a
3zlq.b
4bel.a
[1] 2ewy.a
0
.06 .18 .14 .15 .12
[1] 3zkm.b .06
0
.16 .13 .15 .10
[1] 3zkn.b .18 .16
0
.27 .11 .18
[1] 3zl7.a .14 .13 .27
0
.17 .09
[1] 3zlq.b .15 .15 .11 .17
0
.12
[1] 4bel.a .12 .10 .18 .09 .12
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 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
2ewy.a
3zkm.b
3zkn.b
3zl7.a
3zlq.b
4bel.a
[1] 2ewy.a
0
0.6 1.2 0.9 1.3 0.7
[1] 3zkm.b 0.6
0
1.0 0.9 1.4 0.7
[1] 3zkn.b 1.2 1.0
0
1.2 1.0 0.8
[1] 3zl7.a 0.9 0.9 1.2
0
1.1 0.8
[1] 3zlq.b 1.3 1.4 1.0 1.1
0
0.9
[1] 4bel.a 0.7 0.7 0.8 0.8 0.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.9 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
2ewy.a
3zkm.b
3zkn.b
3zl7.a
3zlq.b
4bel.a
[1] 2ewy.a
0
1.2 1.5 1.8 2.0 1.6
[1] 3zkm.b 1.2
0
1.3 1.2 1.7 1.2
[1] 3zkn.b 1.5 1.3
0
1.8 1.4 1.6
[1] 3zl7.a 1.8 1.2 1.8
0
1.6 1.4
[1] 3zlq.b 2.0 1.7 1.4 1.6
0
1.4
[1] 4bel.a 1.6 1.2 1.6 1.4 1.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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