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CDKL2_HUMAN_1_308

Cyclin-dependent kinase-like 2 [Protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CDKL2_HUMAN):D: Protein kinase (10:12, 15, 18, 31, 33, 64, 80:86, 89, 133, 143, 144, 147, 148)10:12, 15, 18, 31, 33, 64, 80:86, 89, 133, 143, 144, 147, 148

Full PDB list

4aaa, 4bbm

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
V
1
0
G
1
1
Y
1
5
V
1
8
A
3
1
V
6
4
F
8
0
E
8
1
F
8
2
V
8
3
D
8
4
H
8
5
T
8
6
D
8
9
L
1
3
3
C
1
4
3
D
1
4
4
F
1
4
7
[1]4aaa.a dki28 . . . . . . . . . . . . . . . . . .
[1]4bbm.a tc031 . . . . . . . . . . . . . . . . . .

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
V
1
0
G
1
1
E
1
2
Y
1
5
V
1
8
A
3
1
K
3
3
V
6
4
F
8
0
E
8
1
F
8
2
V
8
3
D
8
4
H
8
5
T
8
6
D
8
9
L
1
3
3
C
1
4
3
D
1
4
4
F
1
4
7
A
1
4
8
[1]4aaa.a . . . . . . . . . . . . . . . . . . . . .
[1]4bbm.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
4aaa.a:dki
4bbm.a:tc0
[1] 4aaa.a
0
0
[1] 4bbm.a 2.1
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
4aaa.a
4bbm.a
[1] 4aaa.a
0
.10
[1] 4bbm.a .10
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
4aaa.a
4bbm.a
[1] 4aaa.a
0
1.6
[1] 4bbm.a 1.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 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
4aaa.a
4bbm.a
[1] 4aaa.a
0
1.7
[1] 4bbm.a 1.7
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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