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CADH1_HUMAN_155_255_pep

Cadherin-1

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CADH1_HUMAN):D: Cadherin 1 (158:165, 167, 173:176, 251, 253, 256, 258)158:165, 167, 173:176, 251, 253, 256, 258
Metals (Me):Ca

Full PDB list

1o6s, 2o72, 2omt, 2omu, 2omv, 2omx, 2omy, 2omz, 3ff7, 3ff8, 4zt1, 4zte (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
I
1
5
8
P
1
5
9
P
1
6
0
I
1
6
1
S
1
6
2
C
1
6
3
P
1
6
4
K
1
7
3
L
1
7
5
T
2
5
3
[1]2omv.b E9 . . . . . . . . . . Ca
[1]2omx.b none . . . . . . . . . .
[1]2omy.b E-D17 . . . . . . . . . . Ca
[2]2o72.a none . . . . . S . . . . Ca
[2]4zte.a 4rl,4rl82 . . . . . . . . . . Ca
[3]3ff7.a E-Q18 . . . . . L . . . .
[3]3ff7.b F-Q20 . . . . . L . . . .
[4]3ff8.a F-L-Q28 . . . . . L . . . . Ca

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 Me
I
1
5
8
P
1
5
9
P
1
6
0
I
1
6
1
S
1
6
2
C
1
6
3
P
1
6
4
E
1
6
5
E
1
6
7
K
1
7
3
N
1
7
4
L
1
7
5
V
1
7
6
T
2
5
1
T
2
5
3
N
2
5
6
N
2
5
8
[1]2omv.b . * * . . . . . . . . . . . . - - Ca
[1]2omx.b . * * . . . . . . . . . . . . . .
[1]2omy.b . * * . . . . . . . . . . . . - - Ca
[2]2o72.a . . . . . S . . . . . . . . . . . Ca
[2]4zte.a . . . . . . . . . . . . . . . . . Ca
[3]3ff7.a . * * * * L . - - . . . . . . - -
[3]3ff7.b . * * * * L * . - . . . . . . - -
[4]3ff8.a . * * * * L . . . . . . . . . - - Ca

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
2omv.b:E
2omx.b is apo
2omy.b:E-D
2o72.a is apo
4zte.a:4rl
3ff7.a:E-Q
3ff7.b:F-Q
3ff8.a:F-L-Q
[1] 2omv.b
0
- 0 - 6.0 0.4 0.6 0.2
[1] 2omx.b 0
-
0 - 5.1 0.5 0.8 0.2
[1] 2omy.b 0 -
0
- 6.3 0.8 0.9 0.4
[2] 2o72.a 0 - 0
-
0.5 0 0.3 0.1
[2] 4zte.a 0 - 0 -
0.2
0 0.1 0
[3] 3ff7.a 0 - 0 - 11
0
0 0
[3] 3ff7.b 0 - 0 - 11 0.1
0
0
[4] 3ff8.a 0 - 0 - 10 0.1 0.4
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (4 clusters)

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
2omv.b
2omx.b
2omy.b
2o72.a
4zte.a
3ff7.a
3ff7.b
3ff8.a
[1] 2omv.b
0
.05 .05 .32 .34 .51 .51 .36
[1] 2omx.b .05
0
.08 .28 .29 .52 .52 .37
[1] 2omy.b .05 .08
0
.34 .35 .55 .55 .41
[2] 2o72.a .32 .28 .34
0
.03 .62 .62 .56
[2] 4zte.a .34 .29 .35 .03
0
.65 .65 .59
[3] 3ff7.a .51 .52 .55 .62 .65
0
.16 .24
[3] 3ff7.b .51 .52 .55 .62 .65 .16
0
.28
[4] 3ff8.a .36 .37 .41 .56 .59 .24 .28
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.2 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
2omv.b
2omx.b
2omy.b
2o72.a
4zte.a
3ff7.a
3ff7.b
3ff8.a
[1] 2omv.b
0
0.4 0.3 1.9 1.8 2.2 2.6 1.0
[1] 2omx.b 0.4
0
0.4 5.8 5.7 2.3 2.7 1.1
[1] 2omy.b 0.3 0.4
0
1.8 1.7 2.3 2.7 1.1
[2] 2o72.a 1.9 5.8 1.8
0
0.4 3.3 3.5 2.4
[2] 4zte.a 1.8 5.7 1.7 0.4
0
3.3 3.4 2.4
[3] 3ff7.a 2.2 2.3 2.3 3.3 3.3
0
0.7 1.7
[3] 3ff7.b 2.6 2.7 2.7 3.5 3.4 0.7
0
2.4
[4] 3ff8.a 1.0 1.1 1.1 2.4 2.4 1.7 2.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.9 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
2omv.b
2omx.b
2omy.b
2o72.a
4zte.a
3ff7.a
3ff7.b
3ff8.a
[1] 2omv.b
0
0.8 0.7 2.2 2.1 2.3 2.6 1.3
[1] 2omx.b 0.8
0
0.9 6.2 6.1 2.3 2.6 1.4
[1] 2omy.b 0.7 0.9
0
2.1 2.0 2.4 2.6 1.4
[2] 2o72.a 2.2 6.2 2.1
0
0.6 3.6 3.7 2.7
[2] 4zte.a 2.1 6.1 2.0 0.6
0
3.6 3.7 2.7
[3] 3ff7.a 2.3 2.3 2.4 3.6 3.6
0
1.0 1.8
[3] 3ff7.b 2.6 2.6 2.6 3.7 3.7 1.0
0
2.4
[4] 3ff8.a 1.3 1.4 1.4 2.7 2.7 1.8 2.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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