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LIMK2_HUMAN_330_632

LIM domain kinase 2 [Protein kinase superfamily. TKL Ser/Thr protein kinase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (LIMK2_HUMAN):D: Protein kinase (342, 358, 360:364, 380, 383, 388, 389, 391, 403, 405, 442, 447, 449, 467:470, 472, 474)342, 358, 360:364, 380, 383, 388, 389, 391, 403, 405, 442, 447, 449, 467:470, 472, 474

Full PDB list

4tpt, 5nxd

Pocket contact map

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PDB.ch
   
ligand
A1
V
3
5
8
K
3
6
0
E
3
6
1
L
3
6
2
I
3
6
3
M
3
8
0
L
3
8
3
V
3
8
8
L
3
8
9
F
3
9
1
L
4
0
3
T
4
0
5
L
4
4
2
I
4
4
7
H
4
4
9
V
4
6
7
A
4
6
8
D
4
6
9
F
4
7
0
L
4
7
2
R
4
7
4
[1]4tpt.a 35h31 . . . . . . . . . . . . . . . . . . . . .
[1]5nxd.b 9d830 . . . . . . . . . . . . . . . . . . . . .

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
F
3
4
2
V
3
5
8
K
3
6
0
E
3
6
1
L
3
6
2
I
3
6
3
R
3
6
4
M
3
8
0
L
3
8
3
V
3
8
8
L
3
8
9
F
3
9
1
L
4
0
3
T
4
0
5
L
4
4
2
I
4
4
7
H
4
4
9
V
4
6
7
A
4
6
8
D
4
6
9
F
4
7
0
L
4
7
2
R
4
7
4
[1]4tpt.a . . . . . . . . . . . . . . . . . . . . . . .
[1]5nxd.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
4tpt.a:35h
5nxd.b:9d8
[1] 4tpt.a
0
0.2
[1] 5nxd.b 1.4
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
4tpt.a
5nxd.b
[1] 4tpt.a
0
.07
[1] 5nxd.b .07
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
4tpt.a
5nxd.b
[1] 4tpt.a
0
1.4
[1] 5nxd.b 1.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 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
4tpt.a
5nxd.b
[1] 4tpt.a
0
2.4
[1] 5nxd.b 2.4
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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