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DPP4_RAT_38_767

Dipeptidyl peptidase 4 [Peptidase S9B family. DPPIV subfamily]

Composition of the binding site

Protein chains monomer
A1 (DPP4_RAT):123, 203:207, 355, 356, 548, 550, 630:632, 657, 660, 663, 667, 711, 712, 741123, 203:207, 355, 356, 548, 550, 630:632, 657, 660, 663, 667, 711, 712, 741

Full PDB list

2gbc, 2gbf, 2gbg, 2gbi, 2i3z, 2oae, 4ffv, 4ffw (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
R
1
2
3
E
2
0
3
E
2
0
4
I
2
0
5
F
2
0
6
G
2
0
7
F
3
5
5
R
3
5
6
Y
5
4
8
G
5
5
0
W
6
3
0
S
6
3
1
Y
6
3
2
V
6
5
7
Y
6
6
3
Y
6
6
7
N
7
1
1
V
7
1
2
H
7
4
1
[1]2gbf.a aia18 . . . . . . . . . . . * . . . . . . .
[1]2gbg.a 1ad19 . . . . . . . . . . . * . . . . . . .
[1]2gbi.a xih29 . . . . . . . . . . . . . . . . . . .
[1]2i3z.a lir27 . . . . . . . . . . . . . . . . . . .
[1]2oae.a ail21 . . . . . . . . . . . . . . . . . . .
[1]4ffv.b none . . . . . . . . . . . . . . . . . . .
[1]4ffw.a 71528 . . . . . . . . . . . . . . . . . . .

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
R
1
2
3
E
2
0
3
E
2
0
4
I
2
0
5
F
2
0
6
G
2
0
7
F
3
5
5
R
3
5
6
Y
5
4
8
G
5
5
0
W
6
3
0
S
6
3
1
Y
6
3
2
V
6
5
7
W
6
6
0
Y
6
6
3
Y
6
6
7
N
7
1
1
V
7
1
2
H
7
4
1
[1]2gbf.a . . . . . . . . . . . * . . . . . . . .
[1]2gbg.a . . . . . . . . * . . * . . . . . . . .
[1]2gbi.a . . . . . . . . . . . . . . . . . . . .
[1]2i3z.a . . . . . . . . . . . . . . . . . . . .
[1]2oae.a . . . . . . . . * . . * . . . . . . . .
[1]4ffv.b . . . . . . . * * . . * . . . . . . . .
[1]4ffw.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
2gbf.a:aia
2gbg.a:1ad
2gbi.a:xih
2i3z.a:lir
2oae.a:ail
4ffv.b is apo
4ffw.a:715
[1] 2gbf.a
0.7
0.9 0.5 0.6 0.2 - 0.2
[1] 2gbg.a 0.8
0.6
3.1 2.7 0.2 - 0.1
[1] 2gbi.a 0.4 0.9
0.1
0.3 0.4 - 0.6
[1] 2i3z.a 0.7 1.1 0.2
0.1
0.3 - 0.5
[1] 2oae.a 1.1 1.2 2.9 2.5
0
- 0.5
[1] 4ffv.b 1.5 1.8 2.7 2.4 2.5
-
2.0
[1] 4ffw.a 0.9 1.3 2.9 2.3 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
2gbf.a
2gbg.a
2gbi.a
2i3z.a
2oae.a
4ffv.b
4ffw.a
[1] 2gbf.a
0
.13 .07 .08 .15 .24 .14
[1] 2gbg.a .13
0
.19 .19 .06 .14 .05
[1] 2gbi.a .07 .19
0
.04 .19 .22 .17
[1] 2i3z.a .08 .19 .04
0
.19 .23 .16
[1] 2oae.a .15 .06 .19 .19
0
.16 .04
[1] 4ffv.b .24 .14 .22 .23 .16
0
.16
[1] 4ffw.a .14 .05 .17 .16 .04 .16
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
2gbf.a
2gbg.a
2gbi.a
2i3z.a
2oae.a
4ffv.b
4ffw.a
[1] 2gbf.a
0
0.2 0.2 0.4 0.5 0.3 0.3
[1] 2gbg.a 0.2
0
0.3 0.5 0.5 0.3 0.3
[1] 2gbi.a 0.2 0.3
0
0.5 0.5 0.3 0.4
[1] 2i3z.a 0.4 0.5 0.5
0
0.3 0.5 0.5
[1] 2oae.a 0.5 0.5 0.5 0.3
0
0.5 0.5
[1] 4ffv.b 0.3 0.3 0.3 0.5 0.5
0
0.3
[1] 4ffw.a 0.3 0.3 0.4 0.5 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
2gbf.a
2gbg.a
2gbi.a
2i3z.a
2oae.a
4ffv.b
4ffw.a
[1] 2gbf.a
0
0.5 0.3 0.4 0.6 1.0 1.0
[1] 2gbg.a 0.5
0
0.6 0.6 0.4 1.0 0.9
[1] 2gbi.a 0.3 0.6
0
0.4 0.7 1.1 1.0
[1] 2i3z.a 0.4 0.6 0.4
0
0.6 1.1 1.0
[1] 2oae.a 0.6 0.4 0.7 0.6
0
1.0 0.9
[1] 4ffv.b 1.0 1.0 1.1 1.1 1.0
0
0.7
[1] 4ffw.a 1.0 0.9 1.0 1.0 0.9 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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