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LIMK1_HUMAN_328_638

LIM domain kinase 1 [Protein kinase superfamily. TKL Ser/Thr protein kinase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (LIMK1_HUMAN):D: Protein kinase (345:353, 366, 368, 384, 397, 413:417, 419, 420, 460, 464, 465, 467, 478, 481, 511, 512)345:353, 366, 368, 384, 397, 413:417, 419, 420, 460, 464, 465, 467, 478, 481, 511, 512

Full PDB list

3s95, 5hvj, 5hvk, 5l6w, 5nxc

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
3
4
5
G
3
4
6
K
3
4
7
G
3
4
8
C
3
4
9
F
3
5
0
G
3
5
1
Q
3
5
2
A
3
5
3
V
3
6
6
K
3
6
8
E
3
8
4
L
3
9
7
T
4
1
3
E
4
1
4
Y
4
1
5
I
4
1
6
G
4
1
9
T
4
2
0
D
4
6
0
H
4
6
4
N
4
6
5
L
4
6
7
D
4
7
8
L
4
8
1
N
5
1
2
[1]3s95.b stu35 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5hvj.a anp19 . . . . . . . . . . . . . . . . . . . N . . . . . .
[1]5hvj.b none . . . . . . . . . . . . . . . . . . . N . . . . . .
[1]5hvk.a anp,mg,sep38 . . . . . . . . . . . . . . . . . . . N . . . . . .
[1]5hvk.c anp,mg32 . . . . . . . . . . . . . . . . . . . N . . . . . .
[1]5l6w.l ags31 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5nxc.l 9db31 . . . . . . . . . . . . . . . . . . . . . . . . - .

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
3
4
5
G
3
4
6
K
3
4
7
G
3
4
8
C
3
4
9
F
3
5
0
G
3
5
1
Q
3
5
2
A
3
5
3
V
3
6
6
K
3
6
8
E
3
8
4
L
3
9
7
T
4
1
3
E
4
1
4
Y
4
1
5
I
4
1
6
K
4
1
7
G
4
1
9
T
4
2
0
D
4
6
0
H
4
6
4
N
4
6
5
L
4
6
7
D
4
7
8
L
4
8
1
G
5
1
1
N
5
1
2
[1]3s95.b . . . . . . . . . . * . . . . . . . . . . . . . . . . .
[1]5hvj.a . . . . . . . . . . * . . . . . . . . . N . . . . . . .
[1]5hvj.b . . . . . . . . . . * . . . . . . . . . N . . . . . . *
[1]5hvk.a . . . . . . . . . . * . . . . . . . . . N . . . . . . .
[1]5hvk.c . . . . . . . . . . * . . . . . . . . . N . . . . . . .
[1]5l6w.l . . . . . . . . . . * . . . . . . . . . . . . . . . . .
[1]5nxc.l . . . . . . . . . . . . . . . . . . . . . * . . * - . .

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
3s95.b:stu
5hvj.a:anp
5hvj.b is apo
5hvk.a:anp,mg,sep
5hvk.c:anp,mg
5l6w.l:ags
5nxc.l:9db
[1] 3s95.b
0
0 - 1.3 0.3 0.4 1.2
[1] 5hvj.a 0.5
0
- 0.3 0 0 1.2
[1] 5hvj.b 1.5 0
-
1.7 0.2 0.2 0.3
[1] 5hvk.a 0.5 0 -
0.1
0.1 0.1 1.2
[1] 5hvk.c 1.9 0 - 0.2
0
0.3 0.3
[1] 5l6w.l 1.0 0 - 0.5 0.5
0.3
1.0
[1] 5nxc.l 3.2 0 - 1.6 0.8 1.1
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
3s95.b
5hvj.a
5hvj.b
5hvk.a
5hvk.c
5l6w.l
5nxc.l
[1] 3s95.b
0
.07 .09 .06 .09 .05 .17
[1] 5hvj.a .07
0
.07 .03 .06 .06 .16
[1] 5hvj.b .09 .07
0
.08 .10 .10 .22
[1] 5hvk.a .06 .03 .08
0
.05 .05 .17
[1] 5hvk.c .09 .06 .10 .05
0
.09 .19
[1] 5l6w.l .05 .06 .10 .05 .09
0
.14
[1] 5nxc.l .17 .16 .22 .17 .19 .14
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 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
3s95.b
5hvj.a
5hvj.b
5hvk.a
5hvk.c
5l6w.l
5nxc.l
[1] 3s95.b
0
1.2 1.8 1.1 1.2 1.1 2.3
[1] 5hvj.a 1.2
0
1.2 1.4 1.4 1.2 2.6
[1] 5hvj.b 1.8 1.2
0
1.6 1.7 1.2 3.0
[1] 5hvk.a 1.1 1.4 1.6
0
0.6 1.3 2.9
[1] 5hvk.c 1.2 1.4 1.7 0.6
0
1.5 2.8
[1] 5l6w.l 1.1 1.2 1.2 1.3 1.5
0
2.6
[1] 5nxc.l 2.3 2.6 3.0 2.9 2.8 2.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.3 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
3s95.b
5hvj.a
5hvj.b
5hvk.a
5hvk.c
5l6w.l
5nxc.l
[1] 3s95.b
0
1.2 1.9 1.2 1.3 1.1 2.9
[1] 5hvj.a 1.2
0
1.6 1.7 1.5 1.2 3.1
[1] 5hvj.b 1.9 1.6
0
1.9 1.9 1.4 3.4
[1] 5hvk.a 1.2 1.7 1.9
0
1.1 1.4 3.4
[1] 5hvk.c 1.3 1.5 1.9 1.1
0
1.4 3.3
[1] 5l6w.l 1.1 1.2 1.4 1.4 1.4
0
3.1
[1] 5nxc.l 2.9 3.1 3.4 3.4 3.3 3.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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