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DPP4_PIG_39_766

Dipeptidyl peptidase 4 [Peptidase S9B family. DPPIV subfamily]

Composition of the binding site

Protein chains monomer
A1 (DPP4_PIG):125, 205:207, 209, 357, 358, 547, 552, 629:631, 656, 659, 662, 666, 710, 711, 740125, 205:207, 209, 357, 358, 547, 552, 629:631, 656, 659, 662, 666, 710, 711, 740

Full PDB list

1orv, 1orw, 2aj8, 2ajb, 2ajc, 2ajd, 2bua, 2buc, 5lls

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
R
1
2
5
E
2
0
5
E
2
0
6
V
2
0
7
S
2
0
9
F
3
5
7
R
3
5
8
Y
5
4
7
W
6
2
9
S
6
3
0
Y
6
3
1
V
6
5
6
W
6
5
9
Y
6
6
2
Y
6
6
6
N
7
1
0
V
7
1
1
H
7
4
0
[1]1orv.b none . . . . . . . . . . . . . . . . . .
[1]1orw.a phi.p2y19 . . . . . . . . . * . . . . . . . .
[1]2aj8.a sc326 . . . . . . . . . . . . . . . . . .
[1]2ajb.a 0qg15 . . . . . . . . . * . . . . . . . .
[1]2ajc.b aes12 . . . . . . . * . . . . . . . . . .
[1]2ajd.a bpr15 . . . . . . . . . * . . . . . . . .
[1]2bua.a 00713 . . . . . . . . . . . . . . . . . .
[1]2buc.a 00826 . . . . . . . . . . . . . . . . . .
[1]5lls.a 6z828 . . . . . . . . . . . . . . . . . .

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
R
1
2
5
E
2
0
5
E
2
0
6
V
2
0
7
S
2
0
9
F
3
5
7
R
3
5
8
Y
5
4
7
S
5
5
2
W
6
2
9
S
6
3
0
Y
6
3
1
V
6
5
6
W
6
5
9
Y
6
6
2
Y
6
6
6
N
7
1
0
V
7
1
1
H
7
4
0
[1]1orv.b . . . . . . * * . . * . . . . . . . .
[1]1orw.a . . . . . . * * . . * . . . . . . . .
[1]2aj8.a . . . . . . * . . . . . . . . . . . .
[1]2ajb.a . . . . . . * * . . * . . . . . . . .
[1]2ajc.b . . . . . . * * . . * . . . . . . . .
[1]2ajd.a . . . . . . * * . . * . . . . . . . .
[1]2bua.a . . . . . . * * . . . . . . . . . . .
[1]2buc.a . . . . . . . * . . . . . . . . . . .
[1]5lls.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
1orv.b is apo
1orw.a:phi.p2y
2aj8.a:sc3
2ajb.a:0qg
2ajc.b:aes
2ajd.a:bpr
2bua.a:007
2buc.a:008
5lls.a:6z8
[1] 1orv.b
-
2.2 2.7 1.3 0.2 0.7 0.2 2.7 2.3
[1] 1orw.a -
0.9
2.6 0.6 0 0.7 0.1 1.6 2.4
[1] 2aj8.a - 1.5
0.1
0.5 0.7 0.3 0.1 2.2 0
[1] 2ajb.a - 1.7 2.4
0.6
0.2 0.7 0.1 2.0 2.3
[1] 2ajc.b - 1.8 0.4 0.7
0.6
0.6 0.1 2.3 0.1
[1] 2ajd.a - 1.9 2.3 0.6 0.2
0.5
0.2 1.9 2.3
[1] 2bua.a - 1.8 1.3 0.6 0.2 0.3
0
2.1 1.5
[1] 2buc.a - 0.8 2.3 0.4 0.1 0.4 0
0
2.3
[1] 5lls.a - 0.6 0.1 0.8 0.6 0.5 0.2 0.2
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
1orv.b
1orw.a
2aj8.a
2ajb.a
2ajc.b
2ajd.a
2bua.a
2buc.a
5lls.a
[1] 1orv.b
0
.09 .14 .05 .12 .07 .11 .18 .24
[1] 1orw.a .09
0
.17 .05 .16 .04 .12 .11 .20
[1] 2aj8.a .14 .17
0
.15 .04 .14 .07 .23 .12
[1] 2ajb.a .05 .05 .15
0
.14 .03 .09 .14 .23
[1] 2ajc.b .12 .16 .04 .14
0
.14 .08 .25 .14
[1] 2ajd.a .07 .04 .14 .03 .14
0
.09 .13 .21
[1] 2bua.a .11 .12 .07 .09 .08 .09
0
.16 .18
[1] 2buc.a .18 .11 .23 .14 .25 .13 .16
0
.13
[1] 5lls.a .24 .20 .12 .23 .14 .21 .18 .13
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
1orv.b
1orw.a
2aj8.a
2ajb.a
2ajc.b
2ajd.a
2bua.a
2buc.a
5lls.a
[1] 1orv.b
0
0.2 0.2 0.2 0.1 0.3 0.2 0.2 0.2
[1] 1orw.a 0.2
0
0.3 0.2 0.2 0.3 0.2 0.3 0.3
[1] 2aj8.a 0.2 0.3
0
0.2 0.2 0.3 0.2 0.3 0.2
[1] 2ajb.a 0.2 0.2 0.2
0
0.2 0.2 0.2 0.3 0.3
[1] 2ajc.b 0.1 0.2 0.2 0.2
0
0.3 0.2 0.3 0.2
[1] 2ajd.a 0.3 0.3 0.3 0.2 0.3
0
0.3 0.4 0.4
[1] 2bua.a 0.2 0.2 0.2 0.2 0.2 0.3
0
0.3 0.2
[1] 2buc.a 0.2 0.3 0.3 0.3 0.3 0.4 0.3
0
0.3
[1] 5lls.a 0.2 0.3 0.2 0.3 0.2 0.4 0.2 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

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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
1orv.b
1orw.a
2aj8.a
2ajb.a
2ajc.b
2ajd.a
2bua.a
2buc.a
5lls.a
[1] 1orv.b
0
0.4 0.6 0.3 0.5 0.4 0.3 0.6 0.9
[1] 1orw.a 0.4
0
0.6 0.4 0.7 0.5 0.5 0.7 0.9
[1] 2aj8.a 0.6 0.6
0
0.5 0.3 0.6 0.5 0.8 0.8
[1] 2ajb.a 0.3 0.4 0.5
0
0.6 0.3 0.3 0.7 0.9
[1] 2ajc.b 0.5 0.7 0.3 0.6
0
0.6 0.5 0.8 0.8
[1] 2ajd.a 0.4 0.5 0.6 0.3 0.6
0
0.5 0.7 0.9
[1] 2bua.a 0.3 0.5 0.5 0.3 0.5 0.5
0
0.7 0.8
[1] 2buc.a 0.6 0.7 0.8 0.7 0.8 0.7 0.7
0
0.7
[1] 5lls.a 0.9 0.9 0.8 0.9 0.8 0.9 0.8 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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