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DPP2_HUMAN_27_492

Dipeptidyl peptidase 2 [Peptidase S28 family]

Composition of the binding site

Protein chains monomer
A1 (DPP2_HUMAN):78, 162, 163, 166, 188, 271, 334, 336, 337, 347, 420, 44378, 162, 163, 166, 188, 271, 334, 336, 337, 347, 420, 443

Full PDB list

3jyh, 3n0t, 4ebb

Pocket contact map

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PDB.ch
   
ligand
A1
E
7
8
S
1
6
2
P
1
8
8
M
2
7
1
D
3
3
4
T
3
3
6
G
3
3
7
W
3
4
7
W
4
2
0
H
4
4
3
[1]3jyh.a none . . . . . . . . . .
[1]3n0t.a opy13 . . . . . . . . . .
[1]4ebb.a none . . . * . . . . . .

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
E
7
8
S
1
6
2
Y
1
6
3
M
1
6
6
P
1
8
8
M
2
7
1
D
3
3
4
T
3
3
6
G
3
3
7
W
3
4
7
W
4
2
0
H
4
4
3
[1]3jyh.a . . . . . . . . . . . .
[1]3n0t.a . . . . . . . . . . . .
[1]4ebb.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
3jyh.a is apo
3n0t.a:opy
4ebb.a is apo
[1] 3jyh.a
-
0.2 -
[1] 3n0t.a -
0
-
[1] 4ebb.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
3jyh.a
3n0t.a
4ebb.a
[1] 3jyh.a
0
.02 .03
[1] 3n0t.a .02
0
.05
[1] 4ebb.a .03 .05
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
3jyh.a
3n0t.a
4ebb.a
[1] 3jyh.a
0
0.3 0.2
[1] 3n0t.a 0.3
0
0.4
[1] 4ebb.a 0.2 0.4
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

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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
3jyh.a
3n0t.a
4ebb.a
[1] 3jyh.a
0
0.3 0.5
[1] 3n0t.a 0.3
0
0.6
[1] 4ebb.a 0.5 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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