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CDK1_HUMAN_1_297

Cyclin-dependent kinase 1 [Protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CDK1_HUMAN):D: Protein kinase (10:13, 15, 18, 31, 33, 64, 80:86, 89, 132, 133, 135, 145, 146)10:13, 15, 18, 31, 33, 64, 80:86, 89, 132, 133, 135, 145, 146

Full PDB list

4y72, 4yc3, 5hq0, 5lqf (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
1
0
G
1
1
E
1
2
G
1
3
Y
1
5
V
1
8
A
3
1
K
3
3
V
6
4
F
8
0
E
8
1
F
8
2
L
8
3
S
8
4
M
8
5
D
8
6
K
8
9
Q
1
3
2
N
1
3
3
L
1
3
5
D
1
4
6
[1]4y72.a lz926 . . . . . . . . . . . . . . . . . . . . .
[1]4yc3.a none . . . . . . . . . . . . . . . . . . . . .
[1]5lqf.d 4sp28 . . . . . . . . . . . . . . . . . . . . .

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
I
1
0
G
1
1
E
1
2
G
1
3
Y
1
5
V
1
8
A
3
1
K
3
3
V
6
4
F
8
0
E
8
1
F
8
2
L
8
3
S
8
4
M
8
5
D
8
6
K
8
9
Q
1
3
2
N
1
3
3
L
1
3
5
A
1
4
5
D
1
4
6
[1]4y72.a . . . . . . . . . . . . . . . . . . . . . .
[1]4yc3.a . . . . . . . . . . . . . . . . . . . . . .
[1]5lqf.d . . . . . . . . . . . . . . . . . . . . . .

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
4y72.a:lz9
4yc3.a is apo
5lqf.d:4sp
[1] 4y72.a
0
- 1.0
[1] 4yc3.a 0.3
-
0.5
[1] 5lqf.d 0.2 -
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
4y72.a
4yc3.a
5lqf.d
[1] 4y72.a
0
.05 .05
[1] 4yc3.a .05
0
.03
[1] 5lqf.d .05 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.5 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
4y72.a
4yc3.a
5lqf.d
[1] 4y72.a
0
1.3 0.6
[1] 4yc3.a 1.3
0
1.4
[1] 5lqf.d 0.6 1.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
4y72.a
4yc3.a
5lqf.d
[1] 4y72.a
0
1.5 1.9
[1] 4yc3.a 1.5
0
2.2
[1] 5lqf.d 1.9 2.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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