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CASP8_HUMAN_219_478

Caspase-8 [Peptidase C14A family]

Composition of the binding site

Protein chains monomer
A1 (CASP8_HUMAN):254:258, 260, 261, 316:318, 324, 358:360, 363, 365, 410:416, 419, 420, 455, 457, 458254:258, 260, 261, 316:318, 324, 358:360, 363, 365, 410:416, 419, 420, 455, 457, 458

Full PDB list

1f9e, 1i4e, 1qdu, 1qtn, 2c2z, 2fun, 2y1l, 3h11, 3kjn, 3kjq, 4jj7, 4prz, 4ps1

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
2
5
4
I
2
5
7
R
2
5
8
R
2
6
0
N
2
6
1
S
3
1
6
H
3
1
7
G
3
1
8
Y
3
2
4
Q
3
5
8
A
3
5
9
C
3
6
0
Y
3
6
5
V
4
1
0
S
4
1
1
Y
4
1
2
R
4
1
3
N
4
1
4
P
4
1
5
A
4
1
6
T
4
1
9
W
4
2
0
D
4
5
5
K
4
5
7
N
4
5
8
[1]1f9e.c phqDEVasa42 . . . . . . . . . . . * . . . . . . . . . . . . .
[1]1i4e.b CV-YSDQMD64 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1qdu.a phqEVD0qe27 . . . . . . . . . . . * . . . . . . . . . . . . .
[1]1qtn.a aceIETasj35 . . . . . . . . . . . * . - - - - - - - - - - - -
[1]2c2z.a phqLETmx556 . . . . . . . . . . . * . - - - - - - - - - - - -
[1]2fun.d CV-DYSDQMD72 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2y1l.a IETD32 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3h11.b AIETasa37 . . . . . . . . . . . . . . . . . . . . . . - - -
[1]3kjn.a b9343 . . . . . . . . . . . * . - - - - - - - - - - - -
[1]3kjq.a b9429 . . . . . . . . . . . * . - - - - - - - - - - - -
[1]4jj7.a ace.1mhDb3l.hlx.1u849 . . . . . . . . . . . * . . . . . . . . . . . . .
[1]4prz.a aceLET1u836 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ps1.c balLQhyp.1u839 . . . . . . . . . . . . . . . . . . . . . . . . .

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
L
2
5
4
H
2
5
5
S
2
5
6
I
2
5
7
R
2
5
8
R
2
6
0
N
2
6
1
S
3
1
6
H
3
1
7
G
3
1
8
Y
3
2
4
Q
3
5
8
A
3
5
9
C
3
6
0
D
3
6
3
Y
3
6
5
V
4
1
0
S
4
1
1
Y
4
1
2
R
4
1
3
N
4
1
4
P
4
1
5
A
4
1
6
T
4
1
9
W
4
2
0
D
4
5
5
K
4
5
7
N
4
5
8
[1]1f9e.c . . . * . . . . . . . . . * . . . . . . . . . . . . . .
[1]1i4e.b . . . . * . . . . . . . . * . . . . . . . . . . . . . .
[1]1qdu.a . . . . * . . . . . . . . * . . . . . . . . . . . . . .
[1]1qtn.a . . . . * . . . . . . . . * . . - - - - - - - - - - - -
[1]2c2z.a . . . . . . . . . . . . . * . . - - - - - - - - - - - -
[1]2fun.d . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2y1l.a . . . . * . . . . . . . . * . . . . . . . . . . . . . .
[1]3h11.b . . . . * . . . . . . . . * . . . . . . . . . . . - - -
[1]3kjn.a . . . . . . . . . . . . . * . . - - - - - - - - - - - -
[1]3kjq.a . . . . * . . . . . . . . * . . - - - - - - - - - - - -
[1]4jj7.a . . . . . . . . . . . . . * . . . . . . . . . . . . . .
[1]4prz.a . . . . * . . . . . . . . . . . . . . . . . . . . . . .
[1]4ps1.c . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
1f9e.c:phqDEVasa
1i4e.b:CV-YSDQMD
1qdu.a:phqEVD0qe
1qtn.a:aceIETasj
2c2z.a:phqLETmx5
2fun.d:CV-DYSDQMD
2y1l.a:IETD
3h11.b:AIETasa
3kjn.a:b93
3kjq.a:b94
4jj7.a:ace.1mhDb3l.hlx.1u8
4prz.a:aceLET1u8
4ps1.c:balLQhyp.1u8
[1] 1f9e.c
0.5
0.9 0.7 0.4 1.5 0.7 0.4 0.5 0.6 0.6 0.8 0.5 0.7
[1] 1i4e.b 0.6
0.3
0.8 1.1 1.6 0.5 1.0 0.7 1.3 1.1 2.1 1.3 1.4
[1] 1qdu.a 0.4 0.7
0.4
0.4 0.5 0.5 0.2 0.4 0.6 0.6 1.3 0.4 0.8
[1] 1qtn.a 0.6 0.7 0.7
0.4
0.7 0.4 0.2 0.4 0.6 0.6 1.8 0.6 0.9
[1] 2c2z.a 0.3 0.4 0.5 0.3
0.4
0.2 0.2 0.1 0.4 0.6 0.6 0.4 0.6
[1] 2fun.d 0.4 0.7 0.7 0.5 0.8
0.2
0.7 0.5 1.1 0.7 1.2 0.7 0.6
[1] 2y1l.a 0.6 0.9 0.7 0.7 0.9 0.9
0.5
0.4 0.7 0.9 1.8 0.5 1.1
[1] 3h11.b 0.6 0.9 0.9 0.9 0.9 0.5 1.1
0.2
0.9 0.8 1.5 0.7 0.5
[1] 3kjn.a 0.3 0.2 0.4 0.3 0.4 0.2 0.3 0.1
0.4
0.4 0.7 0.4 0.6
[1] 3kjq.a 0.3 0.2 0.4 0.3 0.4 0.1 0.4 0.1 0.6
0.4
1.5 0.4 0.4
[1] 4jj7.a 0.4 0.2 0.5 0.1 0.5 0.3 0.7 0.1 0.4 0.4
0.4
0.4 0.4
[1] 4prz.a 0.3 0.5 0.6 0.3 0.6 0.5 0.9 0.1 0.5 0.6 1.7
0.5
0.4
[1] 4ps1.c 0.4 0.7 0.7 0.4 0.7 0.6 0.9 0.1 1.2 0.7 1.2 0.5
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
1f9e.c
1i4e.b
1qdu.a
1qtn.a
2c2z.a
2fun.d
2y1l.a
3h11.b
3kjn.a
3kjq.a
4jj7.a
4prz.a
4ps1.c
[1] 1f9e.c
0
.10 .06 .08 .04 .12 .09 .10 .04 .06 .07 .11 .11
[1] 1i4e.b .10
0
.07 .05 .09 .07 .08 .06 .09 .05 .09 .06 .08
[1] 1qdu.a .06 .07
0
.04 .05 .09 .04 .09 .04 .04 .08 .09 .08
[1] 1qtn.a .08 .05 .04
0
.05 .09 .03 .10 .06 .03 .09 .07 .09
[1] 2c2z.a .04 .09 .05 .05
0
.08 .07 .09 0 .04 .04 .09 .08
[1] 2fun.d .12 .07 .09 .09 .08
0
.10 .05 .09 .08 .06 .06 .03
[1] 2y1l.a .09 .08 .04 .03 .07 .10
0
.10 .07 .05 .10 .09 .09
[1] 3h11.b .10 .06 .09 .10 .09 .05 .10
0
.09 .06 .08 .06 .04
[1] 3kjn.a .04 .09 .04 .06 0 .09 .07 .09
0
.04 .04 .09 .08
[1] 3kjq.a .06 .05 .04 .03 .04 .08 .05 .06 .04
0
.07 .06 .07
[1] 4jj7.a .07 .09 .08 .09 .04 .06 .10 .08 .04 .07
0
.07 .05
[1] 4prz.a .11 .06 .09 .07 .09 .06 .09 .06 .09 .06 .07
0
.05
[1] 4ps1.c .11 .08 .08 .09 .08 .03 .09 .04 .08 .07 .05 .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.2 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
1f9e.c
1i4e.b
1qdu.a
1qtn.a
2c2z.a
2fun.d
2y1l.a
3h11.b
3kjn.a
3kjq.a
4jj7.a
4prz.a
4ps1.c
[1] 1f9e.c
0
31 0.7 0.8 0.8 31 1.2 27 0.8 0.7 31 31 31
[1] 1i4e.b 31
0
31 0.6 0.5 0.2 30 0.7 0.6 0.5 0.7 0.6 0.7
[1] 1qdu.a 0.7 31
0
0.3 0.3 31 1.1 27 0.3 0.4 31 31 31
[1] 1qtn.a 0.8 0.6 0.3
0
0.3 0.7 0.5 0.6 0.2 0.3 0.4 0.3 0.4
[1] 2c2z.a 0.8 0.5 0.3 0.3
0
0.5 0.6 0.6 0.3 0.2 0.2 0.2 0.2
[1] 2fun.d 31 0.2 31 0.7 0.5
0
30 0.7 0.6 0.6 0.7 0.6 0.7
[1] 2y1l.a 1.2 30 1.1 0.5 0.6 30
0
26 0.5 0.6 30 30 30
[1] 3h11.b 27 0.7 27 0.6 0.6 0.7 26
0
0.6 0.6 0.5 0.5 0.5
[1] 3kjn.a 0.8 0.6 0.3 0.2 0.3 0.6 0.5 0.6
0
0.2 0.2 0.2 0.3
[1] 3kjq.a 0.7 0.5 0.4 0.3 0.2 0.6 0.6 0.6 0.2
0
0.1 0.1 0.2
[1] 4jj7.a 31 0.7 31 0.4 0.2 0.7 30 0.5 0.2 0.1
0
0.2 0.2
[1] 4prz.a 31 0.6 31 0.3 0.2 0.6 30 0.5 0.2 0.1 0.2
0
0.3
[1] 4ps1.c 31 0.7 31 0.4 0.2 0.7 30 0.5 0.3 0.2 0.2 0.3
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
1f9e.c
1i4e.b
1qdu.a
1qtn.a
2c2z.a
2fun.d
2y1l.a
3h11.b
3kjn.a
3kjq.a
4jj7.a
4prz.a
4ps1.c
[1] 1f9e.c
0
31 1.1 1.2 1.5 31 1.4 27 1.1 1.3 31 30 30
[1] 1i4e.b 31
0
31 1.2 1.6 1.0 30 1.3 1.1 1.2 1.1 1.0 1.1
[1] 1qdu.a 1.1 31
0
1.3 1.6 31 1.4 27 1.3 1.4 31 30 30
[1] 1qtn.a 1.2 1.2 1.3
0
1.2 1.1 0.7 1.5 0.3 0.6 0.7 0.5 0.6
[1] 2c2z.a 1.5 1.6 1.6 1.2
0
1.4 1.4 1.7 0.4 1.3 1.0 1.2 1.2
[1] 2fun.d 31 1.0 31 1.1 1.4
0
30 1.4 0.9 1.1 1.1 0.9 1.1
[1] 2y1l.a 1.4 30 1.4 0.7 1.4 30
0
26 0.6 0.9 30 29 29
[1] 3h11.b 27 1.3 27 1.5 1.7 1.4 26
0
1.4 1.4 1.2 1.2 1.1
[1] 3kjn.a 1.1 1.1 1.3 0.3 0.4 0.9 0.6 1.4
0
0.3 0.5 0.3 0.4
[1] 3kjq.a 1.3 1.2 1.4 0.6 1.3 1.1 0.9 1.4 0.3
0
0.7 0.5 0.4
[1] 4jj7.a 31 1.1 31 0.7 1.0 1.1 30 1.2 0.5 0.7
0
0.5 0.7
[1] 4prz.a 30 1.0 30 0.5 1.2 0.9 29 1.2 0.3 0.5 0.5
0
0.5
[1] 4ps1.c 30 1.1 30 0.6 1.2 1.1 29 1.1 0.4 0.4 0.7 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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