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CLK1_HUMAN_147_484

Dual specificity protein kinase CLK1 [Protein kinase superfamily. CMGC Ser/Thr protein kinase family. Lammer subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CLK1_HUMAN):D: Protein kinase (167:170, 172, 175, 189, 191, 206, 225, 241:245, 292, 293, 295, 324, 325)167:170, 172, 175, 189, 191, 206, 225, 241:245, 292, 293, 295, 324, 325

Full PDB list

1z57, 2vag, 5j1v, 5j1w, 5x8i

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
1
6
7
G
1
6
8
E
1
6
9
G
1
7
0
F
1
7
2
V
1
7
5
A
1
8
9
K
1
9
1
V
2
2
5
F
2
4
1
E
2
4
2
L
2
4
3
L
2
4
4
G
2
4
5
E
2
9
2
N
2
9
3
L
2
9
5
V
3
2
4
D
3
2
5
[1]1z57.a dbq18 . . . . . . . . . . . . . . . . . . .
[1]2vag.a v2522 . . . . . . . . . . . . . . . . . . .
[1]5j1v.b 6fd16 . . . . . . . . . . . . . . . . . . .
[1]5j1w.c 6fb15 . . . . . . . . . . . . . . . . . . .
[1]5x8i.b sqz31 . . . . . . . . . . . . . . . . . . .

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
1
6
7
G
1
6
8
E
1
6
9
G
1
7
0
F
1
7
2
V
1
7
5
A
1
8
9
K
1
9
1
E
2
0
6
V
2
2
5
F
2
4
1
E
2
4
2
L
2
4
3
L
2
4
4
G
2
4
5
E
2
9
2
N
2
9
3
L
2
9
5
V
3
2
4
D
3
2
5
[1]1z57.a . . . . . . . * . . . . . . . . . . . *
[1]2vag.a . . . . . . . . . . . . . . . . . . . .
[1]5j1v.b . . . . . . . . . . . . . . . . . . . .
[1]5j1w.c . . . . . . . . . . . . . . . . . . . .
[1]5x8i.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
1z57.a:dbq
2vag.a:v25
5j1v.b:6fd
5j1w.c:6fb
5x8i.b:sqz
[1] 1z57.a
0
0.3 0 0 1.5
[1] 2vag.a 0
0
0.1 0.2 1.2
[1] 5j1v.b 0 0.2
0
0 0.7
[1] 5j1w.c 0 0.3 0
0
1.0
[1] 5x8i.b 0 0.1 0 0.1
0
[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
1z57.a
2vag.a
5j1v.b
5j1w.c
5x8i.b
[1] 1z57.a
0
.04 .04 .02 .08
[1] 2vag.a .04
0
.04 .04 .07
[1] 5j1v.b .04 .04
0
.02 .04
[1] 5j1w.c .02 .04 .02
0
.06
[1] 5x8i.b .08 .07 .04 .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
1z57.a
2vag.a
5j1v.b
5j1w.c
5x8i.b
[1] 1z57.a
0
0.3 0.4 0.4 0.5
[1] 2vag.a 0.3
0
0.5 0.5 0.5
[1] 5j1v.b 0.4 0.5
0
0.2 0.3
[1] 5j1w.c 0.4 0.5 0.2
0
0.3
[1] 5x8i.b 0.5 0.5 0.3 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
1z57.a
2vag.a
5j1v.b
5j1w.c
5x8i.b
[1] 1z57.a
0
0.3 0.4 0.4 0.7
[1] 2vag.a 0.3
0
0.5 0.5 0.7
[1] 5j1v.b 0.4 0.5
0
0.4 0.7
[1] 5j1w.c 0.4 0.5 0.4
0
0.7
[1] 5x8i.b 0.7 0.7 0.7 0.7
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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