If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

CATD_HUMAN_63_411

Cathepsin D [Peptidase A1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CATD_HUMAN):D: Peptidase A1 (95, 97, 99, 100, 141:144, 189, 190, 192, 193, 195, 198, 206, 269, 293, 295, 297:300, 324, 367, 371, 373:376, 379, 382, 384)
77, 78
77, 78, 95, 97, 99, 100, 141:144, 189, 190, 192, 193, 195, 198, 206, 269, 293, 295, 297:300, 324, 367, 371, 373:376, 379, 382, 384

Full PDB list

1lya, 1lyb, 1lyw, 4obz, 4oc6, 4od9 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
A
7
7
Q
7
8
V
9
5
D
9
7
G
9
9
S
1
0
0
H
1
4
1
Y
1
4
2
G
1
4
3
S
1
4
4
T
1
8
9
F
1
9
0
A
1
9
2
A
1
9
3
F
1
9
5
I
1
9
8
I
2
0
6
Y
2
6
9
I
2
9
3
D
2
9
5
G
2
9
7
T
2
9
8
S
2
9
9
E
3
2
4
M
3
7
3
I
3
7
5
P
3
7
6
S
3
7
9
I
3
8
4
[1]1lya.c none . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1lyb.a ivaVVstaAsta48 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4obz.a 2s425 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4oc6.a 2s158 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4od9.a 2rz39 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
A
7
7
Q
7
8
V
9
5
D
9
7
G
9
9
S
1
0
0
H
1
4
1
Y
1
4
2
G
1
4
3
S
1
4
4
T
1
8
9
F
1
9
0
A
1
9
2
A
1
9
3
F
1
9
5
I
1
9
8
I
2
0
6
Y
2
6
9
I
2
9
3
D
2
9
5
G
2
9
7
T
2
9
8
S
2
9
9
L
3
0
0
E
3
2
4
L
3
6
7
M
3
7
1
M
3
7
3
D
3
7
4
I
3
7
5
P
3
7
6
S
3
7
9
L
3
8
2
I
3
8
4
[1]1lya.c . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1lyb.a . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . .
[1]4obz.a . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . .
[1]4oc6.a . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . .
[1]4od9.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

zoom: [−] [+]; [view as image]; [download as text]

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1lya.c is apo
1lyb.a:ivaVVstaAsta
4obz.a:2s4
4oc6.a:2s1
4od9.a:2rz
[1] 1lya.c
-
0.2 0.1 0 0.6
[1] 1lyb.a -
0
0.7 0.3 1.3
[1] 4obz.a - 0.1
0.1
0.1 1.0
[1] 4oc6.a - 0.5 0.9
0
1.0
[1] 4od9.a - 0.5 0.6 0.5
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1lya.c
1lyb.a
4obz.a
4oc6.a
4od9.a
[1] 1lya.c
0
.04 .02 .04 .03
[1] 1lyb.a .04
0
.03 .03 .04
[1] 4obz.a .02 .03
0
.04 .04
[1] 4oc6.a .04 .03 .04
0
.05
[1] 4od9.a .03 .04 .04 .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1lya.c
1lyb.a
4obz.a
4oc6.a
4od9.a
[1] 1lya.c
0
0.6 0.6 0.5 0.7
[1] 1lyb.a 0.6
0
0.7 0.5 0.6
[1] 4obz.a 0.6 0.7
0
0.6 0.5
[1] 4oc6.a 0.5 0.5 0.6
0
0.6
[1] 4od9.a 0.7 0.6 0.5 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1lya.c
1lyb.a
4obz.a
4oc6.a
4od9.a
[1] 1lya.c
0
0.8 0.8 0.8 0.9
[1] 1lyb.a 0.8
0
0.9 0.8 0.9
[1] 4obz.a 0.8 0.9
0
0.8 0.8
[1] 4oc6.a 0.8 0.8 0.8
0
0.9
[1] 4od9.a 0.9 0.9 0.8 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

loading...