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CATC_HUMAN_25_463

Dipeptidyl peptidase 1 [Peptidase C1 family]

Composition of the binding site

Protein chains monomer
A1 (CATC_HUMAN):25:27, 88, 252, 256:259, 299:303, 373, 403:40625:27, 88, 252, 256:259, 299:303, 373, 403:406

Full PDB list

1k3b, 2djf, 2djg, 3pdf, 4cdc, 4cdd, 4cde, 4cdf, 4oel, 4oem (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
D
2
5
T
2
6
P
2
7
Y
8
8
Q
2
5
2
G
2
5
6
S
2
5
7
C
2
5
8
Y
2
5
9
E
2
9
9
G
3
0
0
G
3
0
1
F
3
0
2
P
3
0
3
A
3
7
3
T
4
0
3
N
4
0
4
A
4
0
6
[1]2djf.a 1zb16 . . . . . . . * . . . . . . . - - -
[1]2djg.a none . . . . . . . . . . . . . . . - - -
[1]3pdf.a lxv20 . . . . . . . * . . . . . . . . . .
[1]4cdc.a 6ao23 . . . . . . . * . . . . . . . - - -
[1]4cdd.a gdi27 . . . . . . . * . . . . . . . - - -
[1]4cde.a u6b28 . . . . . . . * . . . . . . . - - -
[1]4cdf.a w2c28 . . . . . . . * . . . . . . . - - -
[1]4oel.a SY18 . . . . . . . * . . . . . . . - - -
[1]4oem.a GK13 . . . . . . . * . . . . . . . - - -

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
2
5
T
2
6
P
2
7
Y
8
8
Q
2
5
2
G
2
5
6
S
2
5
7
C
2
5
8
Y
2
5
9
E
2
9
9
G
3
0
0
G
3
0
1
F
3
0
2
P
3
0
3
A
3
7
3
T
4
0
3
N
4
0
4
H
4
0
5
A
4
0
6
[1]2djf.a * . . . . . . * . . . . . . . - - - -
[1]2djg.a * . . . . . . * . . . . . . . - - - -
[1]3pdf.a . . . . . . . * . . . . . . . . . . .
[1]4cdc.a * . . . . . . * . . . . . . . - - - -
[1]4cdd.a * . . . . . . * . . . . . . . - - - -
[1]4cde.a * . . . . . . * . . . . . . . - - - -
[1]4cdf.a * . . . . . . * . . . . . . . - - - -
[1]4oel.a * . . . . . . * . . . . . . . - - - -
[1]4oem.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
2djf.a:1zb
2djg.a is apo
3pdf.a:lxv
4cdc.a:6ao
4cdd.a:gdi
4cde.a:u6b
4cdf.a:w2c
4oel.a:SY
4oem.a:GK
[1] 2djf.a
0.4
- 2.1 0.5 1.3 0.5 1.2 0.4 0.4
[1] 2djg.a 0.5
-
1.9 0.5 1.3 0.6 1.4 0.6 0.5
[1] 3pdf.a 0.5 -
0.6
1.0 1.2 1.0 0.9 0.8 0.4
[1] 4cdc.a 0.4 - 2.0
0.5
1.3 0.7 1.3 0.6 0.4
[1] 4cdd.a 0.4 - 2.1 0.5
0.4
0.5 0.4 0.4 0.4
[1] 4cde.a 0.4 - 1.9 0.4 1.1
0.4
0.9 0.6 0.4
[1] 4cdf.a 0.4 - 1.9 0.4 0.6 0.5
0.4
0.6 0.4
[1] 4oel.a 0.4 - 2.0 0.5 1.2 0.5 0.9
0.4
0.4
[1] 4oem.a 0.4 - 2.0 0.4 1.5 0.5 0.9 0.6
0.4
[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
2djf.a
2djg.a
3pdf.a
4cdc.a
4cdd.a
4cde.a
4cdf.a
4oel.a
4oem.a
[1] 2djf.a
0
.01 .08 .01 .05 .03 .05 .01 .01
[1] 2djg.a .01
0
.07 .01 .05 .02 .04 .01 0
[1] 3pdf.a .08 .07
0
.07 .07 .06 .06 .07 .07
[1] 4cdc.a .01 .01 .07
0
.05 .02 .04 .01 .01
[1] 4cdd.a .05 .05 .07 .05
0
.04 .01 .04 .05
[1] 4cde.a .03 .02 .06 .02 .04
0
.03 .02 .02
[1] 4cdf.a .05 .04 .06 .04 .01 .03
0
.04 .04
[1] 4oel.a .01 .01 .07 .01 .04 .02 .04
0
.01
[1] 4oem.a .01 0 .07 .01 .05 .02 .04 .01
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
2djf.a
2djg.a
3pdf.a
4cdc.a
4cdd.a
4cde.a
4cdf.a
4oel.a
4oem.a
[1] 2djf.a
0
0.1 0.2 0.2 0.3 0.2 0.3 0.1 0.1
[1] 2djg.a 0.1
0
0.2 0.2 0.3 0.2 0.3 0.1 0.1
[1] 3pdf.a 0.2 0.2
0
0.2 0.3 0.2 0.3 0.2 0.1
[1] 4cdc.a 0.2 0.2 0.2
0
0.2 0.2 0.2 0.2 0.2
[1] 4cdd.a 0.3 0.3 0.3 0.2
0
0.3 0.1 0.2 0.2
[1] 4cde.a 0.2 0.2 0.2 0.2 0.3
0
0.3 0.1 0.1
[1] 4cdf.a 0.3 0.3 0.3 0.2 0.1 0.3
0
0.2 0.3
[1] 4oel.a 0.1 0.1 0.2 0.2 0.2 0.1 0.2
0
0.1
[1] 4oem.a 0.1 0.1 0.1 0.2 0.2 0.1 0.3 0.1
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
2djf.a
2djg.a
3pdf.a
4cdc.a
4cdd.a
4cde.a
4cdf.a
4oel.a
4oem.a
[1] 2djf.a
0
0.6 0.5 0.7 0.8 0.6 0.8 0.2 0.3
[1] 2djg.a 0.6
0
0.8 0.6 0.7 0.4 0.6 0.6 0.6
[1] 3pdf.a 0.5 0.8
0
0.9 1.0 0.7 0.8 0.5 0.5
[1] 4cdc.a 0.7 0.6 0.9
0
0.4 0.6 0.7 0.7 0.8
[1] 4cdd.a 0.8 0.7 1.0 0.4
0
0.7 0.6 0.8 0.9
[1] 4cde.a 0.6 0.4 0.7 0.6 0.7
0
0.5 0.5 0.5
[1] 4cdf.a 0.8 0.6 0.8 0.7 0.6 0.5
0
0.7 0.7
[1] 4oel.a 0.2 0.6 0.5 0.7 0.8 0.5 0.7
0
0.2
[1] 4oem.a 0.3 0.6 0.5 0.8 0.9 0.5 0.7 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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