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CASP1_HUMAN_121_404

Caspase-1 [Peptidase C14A family]

Composition of the binding site

Protein chains monomer
A1 (CASP1_HUMAN):176, 177, 179, 180, 236:238, 283:288, 335:340, 346:348, 377, 381, 383, 385176, 177, 179, 180, 236:238, 283:288, 335:340, 346:348, 377, 381, 383, 385

Full PDB list

1bmq, 1ibc, 1ice, 1rwk, 1rwm, 1rwn, 1rwo, 1rwp, 1rwv, 1rww, 1rwx, 1sc1, 1sc3, 1sc4, 2fqq, 2h48, 2h4w, 2h4y, 2h51, 2h54, 2hbq, 2hbr, 2hby, 2hbz, 3d6f, 3d6h, 3d6m, 3e4c, 3ns7, 5mmv, 5mtk (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
P
1
7
7
R
1
7
9
S
2
3
6
H
2
3
7
G
2
3
8
Q
2
8
3
A
2
8
4
C
2
8
5
[1]1bmq.a mno38 . . . . . . . *
[1]1ibc.a aceWEHasa44 . . . . . . . .
[1]1ice.a aceYVAasa35 . . . . . . . *
[1]1rwk.a 15813 . . . . . . . *
[1]1rwm.a q2y37 . . . . . . . *
[1]1rwn.a 4qb37 . . . . . . . *
[1]1rwo.a bth41 . . . . . . . *
[1]1rwp.a hqc34 . . . . . . . *
[1]1rwv.a 5ph36 . . . . . . . *
[1]1rww.a oqb37 . . . . . . . *
[1]1rwx.a ybh40 . . . . . . . *
[1]1sc3.a mli7 . . . . . . . A
[1]2h4y.a phqVADcf031 . . . . . . . *
[1]2h54.a phqVADcf031 . . . . . . . *
[1]2hbz.a phqVADcf031 . . . . . . . *
[1]3ns7.a 3ns30 . . . . . . . *
[1]5mmv.a we038 . . . . . . . *
[1]5mtk.a n7n35 . . . . . . . *
[2]3e4c.a none . . . . . . . A

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
I
1
7
6
P
1
7
7
R
1
7
9
T
1
8
0
S
2
3
6
H
2
3
7
G
2
3
8
Q
2
8
3
A
2
8
4
C
2
8
5
R
2
8
6
G
2
8
7
D
2
8
8
P
3
3
5
D
3
3
6
N
3
3
7
V
3
3
8
S
3
3
9
W
3
4
0
G
3
4
6
S
3
4
7
V
3
4
8
F
3
7
7
D
3
8
1
R
3
8
3
Q
3
8
5
[1]1bmq.a . . . . . . . . . * . . . - - - - - - - - - - - - -
[1]1ibc.a . . . . . * . . . * . . . - - - - - - - - - - - - -
[1]1ice.a . . . . . * . . . * . . . - - - - - - - - - - - - -
[1]1rwk.a . . . . . * . . . * . . . - - - - - - - - - - - - -
[1]1rwm.a . . . . . * . . . * . . . - - - - - - - - - - - - -
[1]1rwn.a . . . . . * . . . * . . . - - - - - - - - - - - - -
[1]1rwo.a . . . . . * . . . * . . . - - - - - - - - - - - - -
[1]1rwp.a . . . . . * . . . * . . . - - - - - - - - - - - - -
[1]1rwv.a . . . . . * . . . * . . . - - - - - - - - - - - - -
[1]1rww.a . . . . . * . . . * . . . - - - - - - - - - - - - -
[1]1rwx.a . . . . . * . . . * . . . - - - - - - - - - - - - -
[1]1sc3.a . . . . . * . . . A . . . - - - - - - - - - - - - -
[1]2h4y.a . . . . . . . . . * K . . - - - - - - - - - - - - -
[1]2h54.a . . . . . * . . . * . . . - - - - - - - - - - - - -
[1]2hbz.a . . . . . . . . . * A . . - - - - - - - - - - - - -
[1]3ns7.a . . . . . * . . . * . . . - - - - - - - - - - - - -
[1]5mmv.a . . . . . * . . . * . . . - - - - - - - - - - - - -
[1]5mtk.a . . . . . * . . . * . . . - - - - - - - - - - - - -
[2]3e4c.a . . . . . * . . . 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
1bmq.a:mno
1ibc.a:aceWEHasa
1ice.a:aceYVAasa
1rwk.a:158
1rwm.a:q2y
1rwn.a:4qb
1rwo.a:bth
1rwp.a:hqc
1rwv.a:5ph
1rww.a:oqb
1rwx.a:ybh
1sc3.a:mli
2h4y.a:phqVADcf0
2h54.a:phqVADcf0
2hbz.a:phqVADcf0
3ns7.a:3ns
5mmv.a:we0
5mtk.a:n7n
3e4c.a is apo
[1] 1bmq.a
0.4
0.5 0.4 0.9 0.7 0.5 0.9 0.7 0.8 0.6 0.5 0.2 0.9 0.8 0.8 0.5 0.4 0.7 -
[1] 1ibc.a 2.9
0.5
0.6 0.8 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.5 0.8 0.8 0.8 0.4 0.3 0.6 -
[1] 1ice.a 2.6 0.7
0.4
0.9 0.9 0.6 1.0 0.5 1.0 0.6 0.5 0.3 0.9 0.9 0.9 0.7 0.6 0.6 -
[1] 1rwk.a 2.5 0.3 0.1
0.6
0.4 0.1 0.7 0.3 0.4 0.2 0.1 0 0.6 0.6 0.6 0.3 0.1 0.3 -
[1] 1rwm.a 2.6 0.6 0.3 0.7
0.7
0.5 0.8 0.4 0.8 0.4 0.3 0.1 0.7 0.6 0.7 0.6 0.4 0.6 -
[1] 1rwn.a 2.7 0.5 0.4 1.0 0.7
0.4
0.6 0.6 0.7 0.6 0.4 0.2 0.9 0.8 0.8 0.6 0.3 0.6 -
[1] 1rwo.a 2.3 0.2 0.3 0.7 0.5 0.3
0.6
0.3 0.4 0.5 0.3 0.1 0.6 0.6 0.6 0.3 0.3 0.4 -
[1] 1rwp.a 2.3 0.6 0.5 1.0 0.7 0.4 0.6
0.4
0.7 0.6 0.4 0.2 0.8 0.8 0.8 0.7 0.4 0.7 -
[1] 1rwv.a 2.3 0.4 0.3 0.7 0.5 0.3 0.6 0.3
0.4
0.4 0.3 0.1 0.6 0.6 0.6 0.2 0.4 0.4 -
[1] 1rww.a 2.3 0.5 0.4 0.9 0.6 0.6 0.6 0.6 0.6
0.5
0.4 0.4 0.8 0.8 0.8 0.6 0.3 0.6 -
[1] 1rwx.a 2.5 0.6 0.4 1.0 0.7 0.6 0.6 0.6 0.7 0.6
0.4
0.2 0.9 0.8 0.8 0.6 0.3 0.6 -
[1] 1sc3.a 2.5 0.2 0 0.3 0.2 0.1 0.2 0.1 0.3 0.2 0.1
0
0.1 0.1 0.1 0.2 0.1 0.1 -
[1] 2h4y.a 0.4 0.3 0.2 0.7 0.5 0.2 0.4 0.4 0.4 0.3 0.2 0.1
0.4
0.4 0.4 0.3 0.2 0.3 -
[1] 2h54.a 2.5 0.2 0.1 0.7 0.5 0.2 0.4 0.3 0.5 0.3 0.1 0 0.4
0.4
0.4 0.3 0.2 0.3 -
[1] 2hbz.a 0.4 0.2 0.1 0.7 0.5 0.2 0.4 0.3 0.4 0.3 0.1 0.1 0.4 0.4
0.4
0.3 0.2 0.3 -
[1] 3ns7.a 2.7 0.8 0.6 0.9 0.9 0.7 0.9 0.6 0.6 0.5 0.4 0.5 0.9 0.6 0.6
0.4
0.7 0.8 -
[1] 5mmv.a 2.5 0.5 0.4 0.9 0.6 0.4 0.6 0.6 0.9 0.5 0.4 0.3 0.8 0.8 0.8 0.6
0.4
0.6 -
[1] 5mtk.a 2.2 0.7 0.5 0.7 0.5 0.4 0.7 0.4 0.8 0.4 0.4 0.3 0.8 0.8 0.8 0.5 0.3
0.3
-
[2] 3e4c.a 10 9.1 12 4.0 8.2 6.4 8.1 8.3 7.5 7.2 6.9 1.8 8.1 8.7 8.3 8.8 7.5 8.0
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 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
1bmq.a
1ibc.a
1ice.a
1rwk.a
1rwm.a
1rwn.a
1rwo.a
1rwp.a
1rwv.a
1rww.a
1rwx.a
1sc3.a
2h4y.a
2h54.a
2hbz.a
3ns7.a
5mmv.a
5mtk.a
3e4c.a
[1] 1bmq.a
0
.09 .07 .09 .10 .08 .08 .08 .08 .07 .07 .11 .01 .09 .01 .07 .08 .08 .62
[1] 1ibc.a .09
0
.03 .02 .03 .02 .03 .02 .02 .03 .03 .03 .09 .02 .09 .02 .02 .03 .59
[1] 1ice.a .07 .03
0
.02 .03 .01 .01 .01 .01 .01 0 .04 .07 .02 .07 0 .01 .02 .57
[1] 1rwk.a .09 .02 .02
0
0 .01 .01 .02 .02 .02 .02 .03 .08 .01 .08 .03 .01 .02 .58
[1] 1rwm.a .10 .03 .03 0
0
.02 .02 .02 .02 .03 .02 .04 .08 .01 .08 .03 .02 .02 .57
[1] 1rwn.a .08 .02 .01 .01 .02
0
.02 .01 .02 .02 .01 .04 .09 .01 .09 .01 .01 .03 .57
[1] 1rwo.a .08 .03 .01 .01 .02 .02
0
.01 0 .02 .01 .03 .06 .01 .06 .01 .01 .01 .58
[1] 1rwp.a .08 .02 .01 .02 .02 .01 .01
0
.01 .01 0 .04 .07 .02 .07 .01 0 .02 .57
[1] 1rwv.a .08 .02 .01 .02 .02 .02 0 .01
0
.02 .02 .04 .07 .01 .07 .01 .02 .01 .58
[1] 1rww.a .07 .03 .01 .02 .03 .02 .02 .01 .02
0
.01 .05 .07 .02 .07 .02 .01 .01 .56
[1] 1rwx.a .07 .03 0 .02 .02 .01 .01 0 .02 .01
0
.05 .08 .02 .08 .01 .01 .02 .56
[1] 1sc3.a .11 .03 .04 .03 .04 .04 .03 .04 .04 .05 .05
0
.10 .03 .10 .05 .05 .04 .61
[1] 2h4y.a .01 .09 .07 .08 .08 .09 .06 .07 .07 .07 .08 .10
0
.07 0 .08 .08 .06 .63
[1] 2h54.a .09 .02 .02 .01 .01 .01 .01 .02 .01 .02 .02 .03 .07
0
.07 .02 .02 .02 .59
[1] 2hbz.a .01 .09 .07 .08 .08 .09 .06 .07 .07 .07 .08 .10 0 .07
0
.08 .08 .06 .63
[1] 3ns7.a .07 .02 0 .03 .03 .01 .01 .01 .01 .02 .01 .05 .08 .02 .08
0
.01 .02 .57
[1] 5mmv.a .08 .02 .01 .01 .02 .01 .01 0 .02 .01 .01 .05 .08 .02 .08 .01
0
.02 .56
[1] 5mtk.a .08 .03 .02 .02 .02 .03 .01 .02 .01 .01 .02 .04 .06 .02 .06 .02 .02
0
.57
[2] 3e4c.a .62 .59 .57 .58 .57 .57 .58 .57 .58 .56 .56 .61 .63 .59 .63 .57 .56 .57
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
1bmq.a
1ibc.a
1ice.a
1rwk.a
1rwm.a
1rwn.a
1rwo.a
1rwp.a
1rwv.a
1rww.a
1rwx.a
1sc3.a
2h4y.a
2h54.a
2hbz.a
3ns7.a
5mmv.a
5mtk.a
3e4c.a
[1] 1bmq.a
0
0.3 0.4 0.4 0.4 0.3 0.3 0.3 0.3 0.3 0.3 0.4 0.5 0.4 0.5 0.5 0.5 0.5 2.5
[1] 1ibc.a 0.3
0
0.4 0.5 0.5 0.3 0.4 0.3 0.4 0.4 0.3 0.5 0.5 0.5 0.5 0.5 0.4 0.6 2.5
[1] 1ice.a 0.4 0.4
0
0.5 0.5 0.4 0.5 0.4 0.5 0.4 0.4 0.5 0.5 0.5 0.6 0.5 0.5 0.6 2.4
[1] 1rwk.a 0.4 0.5 0.5
0
0.2 0.3 0.2 0.3 0.2 0.3 0.3 0.2 0.3 0.2 0.3 0.5 0.5 0.5 2.7
[1] 1rwm.a 0.4 0.5 0.5 0.2
0
0.3 0.2 0.3 0.2 0.3 0.3 0.2 0.4 0.2 0.4 0.5 0.5 0.4 2.6
[1] 1rwn.a 0.3 0.3 0.4 0.3 0.3
0
0.2 0.1 0.2 0.1 0.1 0.3 0.4 0.3 0.4 0.4 0.3 0.5 2.5
[1] 1rwo.a 0.3 0.4 0.5 0.2 0.2 0.2
0
0.2 0.1 0.3 0.2 0.2 0.3 0.2 0.3 0.5 0.4 0.5 2.6
[1] 1rwp.a 0.3 0.3 0.4 0.3 0.3 0.1 0.2
0
0.2 0.1 0.1 0.3 0.4 0.3 0.4 0.4 0.3 0.5 2.5
[1] 1rwv.a 0.3 0.4 0.5 0.2 0.2 0.2 0.1 0.2
0
0.3 0.2 0.2 0.3 0.2 0.3 0.5 0.4 0.5 2.6
[1] 1rww.a 0.3 0.4 0.4 0.3 0.3 0.1 0.3 0.1 0.3
0
0.2 0.3 0.4 0.4 0.4 0.5 0.3 0.5 2.5
[1] 1rwx.a 0.3 0.3 0.4 0.3 0.3 0.1 0.2 0.1 0.2 0.2
0
0.3 0.4 0.3 0.4 0.4 0.3 0.5 2.5
[1] 1sc3.a 0.4 0.5 0.5 0.2 0.2 0.3 0.2 0.3 0.2 0.3 0.3
0
0.4 0.2 0.4 0.5 0.5 0.5 2.6
[1] 2h4y.a 0.5 0.5 0.5 0.3 0.4 0.4 0.3 0.4 0.3 0.4 0.4 0.4
0
0.3 0.1 0.5 0.5 0.6 2.7
[1] 2h54.a 0.4 0.5 0.5 0.2 0.2 0.3 0.2 0.3 0.2 0.4 0.3 0.2 0.3
0
0.3 0.6 0.5 0.5 2.7
[1] 2hbz.a 0.5 0.5 0.6 0.3 0.4 0.4 0.3 0.4 0.3 0.4 0.4 0.4 0.1 0.3
0
0.5 0.5 0.6 2.7
[1] 3ns7.a 0.5 0.5 0.5 0.5 0.5 0.4 0.5 0.4 0.5 0.5 0.4 0.5 0.5 0.6 0.5
0
0.5 0.7 2.5
[1] 5mmv.a 0.5 0.4 0.5 0.5 0.5 0.3 0.4 0.3 0.4 0.3 0.3 0.5 0.5 0.5 0.5 0.5
0
0.6 2.5
[1] 5mtk.a 0.5 0.6 0.6 0.5 0.4 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.6 0.5 0.6 0.7 0.6
0
2.7
[2] 3e4c.a 2.5 2.5 2.4 2.7 2.6 2.5 2.6 2.5 2.6 2.5 2.5 2.6 2.7 2.7 2.7 2.5 2.5 2.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
1bmq.a
1ibc.a
1ice.a
1rwk.a
1rwm.a
1rwn.a
1rwo.a
1rwp.a
1rwv.a
1rww.a
1rwx.a
1sc3.a
2h4y.a
2h54.a
2hbz.a
3ns7.a
5mmv.a
5mtk.a
3e4c.a
[1] 1bmq.a
0
1.1 1.1 1.0 1.0 1.0 1.0 1.0 1.0 0.9 1.0 1.0 0.8 1.1 0.8 1.1 1.2 1.1 3.3
[1] 1ibc.a 1.1
0
0.6 0.8 0.8 0.7 0.7 0.7 0.8 0.7 0.8 0.8 1.1 0.7 1.1 0.8 0.8 0.8 3.1
[1] 1ice.a 1.1 0.6
0
0.8 0.7 0.7 0.7 0.7 0.8 0.7 0.7 0.7 1.1 0.7 1.1 0.8 0.8 0.8 3.0
[1] 1rwk.a 1.0 0.8 0.8
0
0.2 0.3 0.2 0.3 0.3 0.3 0.3 0.2 1.0 0.4 1.0 0.8 0.7 0.7 3.3
[1] 1rwm.a 1.0 0.8 0.7 0.2
0
0.3 0.2 0.3 0.3 0.3 0.3 0.3 1.0 0.5 1.0 0.8 0.7 0.7 3.3
[1] 1rwn.a 1.0 0.7 0.7 0.3 0.3
0
0.3 0.3 0.4 0.3 0.3 0.3 1.0 0.5 1.0 0.7 0.5 0.7 3.2
[1] 1rwo.a 1.0 0.7 0.7 0.2 0.2 0.3
0
0.3 0.2 0.3 0.3 0.2 1.0 0.4 1.0 0.8 0.7 0.7 3.3
[1] 1rwp.a 1.0 0.7 0.7 0.3 0.3 0.3 0.3
0
0.3 0.2 0.1 0.3 1.0 0.5 1.0 0.7 0.7 0.7 3.2
[1] 1rwv.a 1.0 0.8 0.8 0.3 0.3 0.4 0.2 0.3
0
0.3 0.3 0.3 1.1 0.4 1.1 0.8 0.8 0.7 3.3
[1] 1rww.a 0.9 0.7 0.7 0.3 0.3 0.3 0.3 0.2 0.3
0
0.2 0.3 1.0 0.5 1.0 0.7 0.7 0.7 3.2
[1] 1rwx.a 1.0 0.8 0.7 0.3 0.3 0.3 0.3 0.1 0.3 0.2
0
0.3 1.1 0.6 1.1 0.7 0.7 0.7 3.2
[1] 1sc3.a 1.0 0.8 0.7 0.2 0.3 0.3 0.2 0.3 0.3 0.3 0.3
0
1.1 0.5 1.1 0.8 0.8 0.7 3.3
[1] 2h4y.a 0.8 1.1 1.1 1.0 1.0 1.0 1.0 1.0 1.1 1.0 1.1 1.1
0
1.0 0.1 1.1 1.0 1.1 2.8
[1] 2h54.a 1.1 0.7 0.7 0.4 0.5 0.5 0.4 0.5 0.4 0.5 0.6 0.5 1.0
0
1.0 0.9 0.7 0.7 3.3
[1] 2hbz.a 0.8 1.1 1.1 1.0 1.0 1.0 1.0 1.0 1.1 1.0 1.1 1.1 0.1 1.0
0
1.1 1.1 1.1 2.6
[1] 3ns7.a 1.1 0.8 0.8 0.8 0.8 0.7 0.8 0.7 0.8 0.7 0.7 0.8 1.1 0.9 1.1
0
0.9 0.9 3.2
[1] 5mmv.a 1.2 0.8 0.8 0.7 0.7 0.5 0.7 0.7 0.8 0.7 0.7 0.8 1.0 0.7 1.1 0.9
0
0.8 3.1
[1] 5mtk.a 1.1 0.8 0.8 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 1.1 0.7 1.1 0.9 0.8
0
3.3
[2] 3e4c.a 3.3 3.1 3.0 3.3 3.3 3.2 3.3 3.2 3.3 3.2 3.2 3.3 2.8 3.3 2.6 3.2 3.1 3.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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