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KC1D_HUMAN_1_302

Casein kinase I isoform delta [Protein kinase superfamily. CK1 Ser/Thr protein kinase family. Casein kinase I subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (KC1D_HUMAN):D: Protein kinase (13, 15:19, 21, 23, 25, 36:38, 49, 52, 56, 66, 68, 80:88, 90:92, 95, 132, 135, 138, 148, 149)13, 15:19, 21, 23, 25, 36:38, 49, 52, 56, 66, 68, 80:88, 90:92, 95, 132, 135, 138, 148, 149, 293, 295

Full PDB list

1cki, 1ckj, 3uys, 3uyt, 3uzp, 4hgt, 4hnf, 4jjr, 4kb8, 4kba, 4kbc, 4kbk, 4tn6, 4tw9, 4twc, 5ih4, 5ih5, 5ih6, 5mqv, 5w4w, 5x17 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
1
5
G
1
6
S
1
7
G
1
8
I
2
3
L
2
5
A
3
6
I
3
7
K
3
8
E
5
2
Y
5
6
P
6
6
M
8
0
M
8
2
E
8
3
L
8
4
L
8
5
G
8
6
P
8
7
S
8
8
E
9
0
D
9
1
L
9
2
F
9
5
D
1
3
2
L
1
3
5
L
1
3
8
I
1
4
8
D
1
4
9
L
2
9
3
[1]1ckj.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3uyt.c 0ck25 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4hgt.a 15g28 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4hnf.b 16w25 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4kb8.b 1qo20 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4kb8.c 1qn22 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4kba.c 1qm24 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4kbc.a 1qj20 . . . - . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4kbk.a 1qg25 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4tn6.a pfo31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4tw9.a 386,na37 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4twc.a 37j35 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ih5.a aue20 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ih6.a aug20 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5mqv.b d5q39 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5w4w.a 9wg24 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5x17.b adp27 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . -

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
R
1
3
I
1
5
G
1
6
S
1
7
G
1
8
S
1
9
G
2
1
I
2
3
L
2
5
A
3
6
I
3
7
K
3
8
L
4
9
E
5
2
Y
5
6
P
6
6
I
6
8
M
8
0
V
8
1
M
8
2
E
8
3
L
8
4
L
8
5
G
8
6
P
8
7
S
8
8
E
9
0
D
9
1
L
9
2
F
9
5
D
1
3
2
L
1
3
5
L
1
3
8
I
1
4
8
D
1
4
9
L
2
9
3
F
2
9
5
[1]1ckj.a . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . .
[1]3uyt.c . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . * . . . . . -
[1]4hgt.a . . . . . . . . . . . . . . . . . . . * . . . . . . . . . * . . . . . . -
[1]4hnf.b . * . * . . . . . . . . . . . . . . . * . . . . . . . . . . * . . . * . -
[1]4kb8.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . -
[1]4kb8.c . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . -
[1]4kba.c . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . -
[1]4kbc.a . . . . - - - . . . . . . . . . . . . * . . . . . . . . . . . . . . . . -
[1]4kbk.a . . . . . - . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . -
[1]4tn6.a . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . -
[1]4tw9.a N . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4twc.a N . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ih5.a . . . . . . . . . . . . . . . . . . . * . . . . . . . . . * * . . . . . -
[1]5ih6.a . . . . . . . . . . . . . . . . . . . * . . . . . . . . . * * . . . . . -
[1]5mqv.b . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . -
[1]5w4w.a . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . -
[1]5x17.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - -

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
1ckj.a is apo
3uyt.c:0ck
4hgt.a:15g
4hnf.b:16w
4kb8.b:1qo
4kb8.c:1qn
4kba.c:1qm
4kbc.a:1qj
4kbk.a:1qg
4tn6.a:pfo
4tw9.a:386,na
4twc.a:37j
5ih5.a:aue
5ih6.a:aug
5mqv.b:d5q
5w4w.a:9wg
5x17.b:adp
[1] 1ckj.a
-
1.2 0.6 1.3 1.9 1.1 1.2 1.4 1.5 1.4 1.5 1.3 1.0 1.3 1.3 1.2 1.4
[1] 3uyt.c -
0
1.1 0.6 0.9 0 0 0.1 0.3 0.9 1.1 1.4 0 0 0.2 0.1 0.7
[1] 4hgt.a - 1.5
0
1.4 1.2 1.1 1.2 1.1 1.6 1.7 3.2 2.3 1.2 0.8 1.4 1.7 0.8
[1] 4hnf.b - 0.2 1.6
0
1.1 0.3 0.2 0.2 0.7 0.7 0.9 0.9 0 0 0.8 1.3 1.7
[1] 4kb8.b - 0.4 0.2 0.7
0
0 0.2 0 0.3 0.3 0.2 0 0.1 0.1 0.6 0.4 1.1
[1] 4kb8.c - 0.4 1.7 0.8 1.4
0
0 0.1 0.3 0.2 1.0 1.2 0.1 0.1 0.5 0.1 1.3
[1] 4kba.c - 0.3 1.6 0.7 1.4 0
0
0 0.1 0.3 1.0 1.2 0.1 0.1 0.6 0.3 1.3
[1] 4kbc.a - 0 1.4 0.6 1.0 0 0
0
0.1 0 1.1 1.1 0 0.1 0.1 0.3 0.8
[1] 4kbk.a - 0 1.1 0.4 1.0 0 0 0
0
0.1 0.9 0.9 0.1 0.1 0.1 0.1 1.2
[1] 4tn6.a - 0.1 1.1 0.3 1.0 0 0 0 0.5
0.1
0.9 0.8 0 0.1 0.8 0.3 0.5
[1] 4tw9.a - 1.3 0.5 1.7 0.6 0.8 0.7 0.7 1.5 1.2
0
0 0.7 0.8 1.5 1.3 0.7
[1] 4twc.a - 0.7 0.8 1.5 0.4 0.7 0.6 0.6 1.2 1.2 0.2
0
0.6 0.5 1.7 0.9 1.4
[1] 5ih5.a - 0.6 1.0 0.6 1.3 0.3 0.3 0.4 0.8 1.0 2.1 2.5
0
0.1 0.5 0.5 0.9
[1] 5ih6.a - 1.1 1.2 0.9 1.3 0.2 0.3 0.5 0.8 1.5 2.2 2.5 0.2
0.2
0.6 0.6 1.0
[1] 5mqv.b - 0 1.1 0.6 1.2 0 0 0 0.2 0.5 1.0 1.1 0 0
0
0 1.0
[1] 5w4w.a - 0 1.2 0.6 1.2 0 0 0 0.1 0.4 1.0 1.1 0.2 0.1 0.1
0
1.0
[1] 5x17.b - 0.6 0.1 1.0 0.3 0.3 0.2 0.4 0.9 0.3 0.2 0.2 0.2 0.3 0.8 0.7
0.1
[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
1ckj.a
3uyt.c
4hgt.a
4hnf.b
4kb8.b
4kb8.c
4kba.c
4kbc.a
4kbk.a
4tn6.a
4tw9.a
4twc.a
5ih5.a
5ih6.a
5mqv.b
5w4w.a
5x17.b
[1] 1ckj.a
0
.08 .12 .11 .09 .03 .05 .06 .05 .06 .12 .13 .10 .11 .05 .04 .08
[1] 3uyt.c .08
0
.11 .10 .10 .06 .07 .07 .07 .08 .13 .12 .07 .08 .05 .05 .09
[1] 4hgt.a .12 .11
0
.15 .14 .09 .10 .11 .13 .13 .15 .16 .05 .07 .10 .10 .13
[1] 4hnf.b .11 .10 .15
0
.13 .10 .10 .09 .10 .08 .14 .11 .13 .13 .10 .09 .12
[1] 4kb8.b .09 .10 .14 .13
0
.08 .08 .08 .06 .09 .08 .07 .12 .13 .08 .08 .06
[1] 4kb8.c .03 .06 .09 .10 .08
0
.02 .04 .05 .06 .11 .12 .08 .10 .05 .04 .07
[1] 4kba.c .05 .07 .10 .10 .08 .02
0
.04 .05 .06 .11 .12 .10 .11 .06 .04 .07
[1] 4kbc.a .06 .07 .11 .09 .08 .04 .04
0
.04 .04 .11 .13 .11 .12 .04 .03 .06
[1] 4kbk.a .05 .07 .13 .10 .06 .05 .05 .04
0
.04 .12 .12 .11 .13 .04 .04 .08
[1] 4tn6.a .06 .08 .13 .08 .09 .06 .06 .04 .04
0
.10 .11 .12 .13 .06 .06 .06
[1] 4tw9.a .12 .13 .15 .14 .08 .11 .11 .11 .12 .10
0
.08 .15 .16 .12 .12 .07
[1] 4twc.a .13 .12 .16 .11 .07 .12 .12 .13 .12 .11 .08
0
.15 .13 .11 .12 .09
[1] 5ih5.a .10 .07 .05 .13 .12 .08 .10 .11 .11 .12 .15 .15
0
.03 .09 .09 .12
[1] 5ih6.a .11 .08 .07 .13 .13 .10 .11 .12 .13 .13 .16 .13 .03
0
.11 .11 .13
[1] 5mqv.b .05 .05 .10 .10 .08 .05 .06 .04 .04 .06 .12 .11 .09 .11
0
.02 .08
[1] 5w4w.a .04 .05 .10 .09 .08 .04 .04 .03 .04 .06 .12 .12 .09 .11 .02
0
.08
[1] 5x17.b .08 .09 .13 .12 .06 .07 .07 .06 .08 .06 .07 .09 .12 .13 .08 .08
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.3 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
1ckj.a
3uyt.c
4hgt.a
4hnf.b
4kb8.b
4kb8.c
4kba.c
4kbc.a
4kbk.a
4tn6.a
4tw9.a
4twc.a
5ih5.a
5ih6.a
5mqv.b
5w4w.a
5x17.b
[1] 1ckj.a
0
0.9 0.9 1.0 1.0 0.8 0.8 1.0 1.0 1.7 3.2 3.2 0.7 0.7 0.7 1.2 0.8
[1] 3uyt.c 0.9
0
0.9 0.9 1.0 0.5 0.6 1.0 0.8 1.8 1.2 1.1 0.9 0.9 0.9 1.0 1.0
[1] 4hgt.a 0.9 0.9
0
0.9 1.1 0.7 0.6 1.2 1.1 2.0 1.1 1.1 0.6 0.6 0.7 1.4 0.9
[1] 4hnf.b 1.0 0.9 0.9
0
0.7 0.7 0.7 1.2 0.9 1.9 1.1 1.1 0.8 0.8 1.0 0.9 0.8
[1] 4kb8.b 1.0 1.0 1.1 0.7
0
0.9 0.8 1.0 0.7 1.7 1.2 1.2 0.9 0.9 1.1 0.8 0.8
[1] 4kb8.c 0.8 0.5 0.7 0.7 0.9
0
0.4 1.0 0.8 1.8 1.2 1.1 0.7 0.7 0.7 1.0 0.9
[1] 4kba.c 0.8 0.6 0.6 0.7 0.8 0.4
0
1.0 0.8 1.8 1.1 1.1 0.7 0.7 0.7 1.0 0.8
[1] 4kbc.a 1.0 1.0 1.2 1.2 1.0 1.0 1.0
0
0.8 0.7 1.7 1.7 1.2 1.2 0.9 1.0 0.8
[1] 4kbk.a 1.0 0.8 1.1 0.9 0.7 0.8 0.8 0.8
0
1.5 1.3 1.3 0.9 1.0 0.9 0.7 0.9
[1] 4tn6.a 1.7 1.8 2.0 1.9 1.7 1.8 1.8 0.7 1.5
0
2.2 2.2 1.9 1.9 1.8 1.5 1.4
[1] 4tw9.a 3.2 1.2 1.1 1.1 1.2 1.2 1.1 1.7 1.3 2.2
0
0.5 1.2 1.2 1.6 1.5 0.6
[1] 4twc.a 3.2 1.1 1.1 1.1 1.2 1.1 1.1 1.7 1.3 2.2 0.5
0
1.1 1.1 1.5 1.4 0.8
[1] 5ih5.a 0.7 0.9 0.6 0.8 0.9 0.7 0.7 1.2 0.9 1.9 1.2 1.1
0
0.2 0.8 1.2 0.9
[1] 5ih6.a 0.7 0.9 0.6 0.8 0.9 0.7 0.7 1.2 1.0 1.9 1.2 1.1 0.2
0
0.8 1.2 0.9
[1] 5mqv.b 0.7 0.9 0.7 1.0 1.1 0.7 0.7 0.9 0.9 1.8 1.6 1.5 0.8 0.8
0
1.2 0.9
[1] 5w4w.a 1.2 1.0 1.4 0.9 0.8 1.0 1.0 1.0 0.7 1.5 1.5 1.4 1.2 1.2 1.2
0
1.0
[1] 5x17.b 0.8 1.0 0.9 0.8 0.8 0.9 0.8 0.8 0.9 1.4 0.6 0.8 0.9 0.9 0.9 1.0
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.9 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
1ckj.a
3uyt.c
4hgt.a
4hnf.b
4kb8.b
4kb8.c
4kba.c
4kbc.a
4kbk.a
4tn6.a
4tw9.a
4twc.a
5ih5.a
5ih6.a
5mqv.b
5w4w.a
5x17.b
[1] 1ckj.a
0
1.4 1.2 1.4 1.5 1.4 1.3 1.2 1.5 1.7 3.6 3.5 1.2 1.2 1.1 1.7 1.2
[1] 3uyt.c 1.4
0
1.0 1.1 1.2 1.0 0.9 1.2 1.1 1.8 1.4 1.3 1.2 1.3 1.5 1.3 1.5
[1] 4hgt.a 1.2 1.0
0
1.3 1.4 1.1 1.1 1.4 1.3 2.0 1.4 1.4 0.8 0.8 1.2 1.6 1.3
[1] 4hnf.b 1.4 1.1 1.3
0
1.2 1.1 1.1 1.4 1.2 1.8 1.4 1.4 1.3 1.3 1.5 1.2 1.3
[1] 4kb8.b 1.5 1.2 1.4 1.2
0
1.1 1.1 1.4 0.9 1.7 1.4 1.3 1.3 1.4 1.7 1.0 1.3
[1] 4kb8.c 1.4 1.0 1.1 1.1 1.1
0
0.7 1.4 1.0 1.9 1.4 1.4 1.3 1.4 1.5 1.2 1.4
[1] 4kba.c 1.3 0.9 1.1 1.1 1.1 0.7
0
1.3 1.1 1.8 1.4 1.4 1.3 1.3 1.5 1.3 1.4
[1] 4kbc.a 1.2 1.2 1.4 1.4 1.4 1.4 1.3
0
1.2 0.8 1.8 1.8 1.5 1.5 1.3 1.4 1.3
[1] 4kbk.a 1.5 1.1 1.3 1.2 0.9 1.0 1.1 1.2
0
1.5 1.5 1.5 1.5 1.5 1.6 0.9 1.5
[1] 4tn6.a 1.7 1.8 2.0 1.8 1.7 1.9 1.8 0.8 1.5
0
2.2 2.2 1.9 1.9 1.9 1.6 1.5
[1] 4tw9.a 3.6 1.4 1.4 1.4 1.4 1.4 1.4 1.8 1.5 2.2
0
0.7 1.5 1.5 1.8 1.6 0.8
[1] 4twc.a 3.5 1.3 1.4 1.4 1.3 1.4 1.4 1.8 1.5 2.2 0.7
0
1.4 1.4 1.7 1.6 1.0
[1] 5ih5.a 1.2 1.2 0.8 1.3 1.3 1.3 1.3 1.5 1.5 1.9 1.5 1.4
0
0.2 1.3 1.6 1.2
[1] 5ih6.a 1.2 1.3 0.8 1.3 1.4 1.4 1.3 1.5 1.5 1.9 1.5 1.4 0.2
0
1.3 1.6 1.2
[1] 5mqv.b 1.1 1.5 1.2 1.5 1.7 1.5 1.5 1.3 1.6 1.9 1.8 1.7 1.3 1.3
0
1.8 1.3
[1] 5w4w.a 1.7 1.3 1.6 1.2 1.0 1.2 1.3 1.4 0.9 1.6 1.6 1.6 1.6 1.6 1.8
0
1.5
[1] 5x17.b 1.2 1.5 1.3 1.3 1.3 1.4 1.4 1.3 1.5 1.5 0.8 1.0 1.2 1.2 1.3 1.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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