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PLK2_HUMAN_63_360

Serine/threonine-protein kinase PLK2 [Protein kinase superfamily. Ser/Thr protein kinase family. CDC5/Polo subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PLK2_HUMAN):D: Protein kinase (86:90, 96, 109, 111, 143, 159:163, 165, 169, 212)86:90, 96, 109, 111, 143, 159:163, 165, 169, 212

Full PDB list

4i5m, 4i5p, 4i6b, 4i6f, 4i6h

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
K
8
6
V
8
7
L
8
8
G
8
9
K
9
0
C
9
6
A
1
0
9
K
1
1
1
V
1
4
3
L
1
5
9
E
1
6
0
Y
1
6
1
C
1
6
2
S
1
6
3
R
1
6
5
H
1
6
9
F
2
1
2
[1]4i5m.a r7838 . T . . . . . . . . . . . . . . .
[1]4i5p.a 1d124 . T . . . . . . . . . . . . . . .
[1]4i6b.a 11g19 . T . . . . . . . . . . . . . . .
[1]4i6f.a 1c730 . T . . . . . . . . . . . . . . .
[1]4i6h.a 1c829 . T . . . . . . . . . . . . . . .

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
K
8
6
V
8
7
L
8
8
G
8
9
K
9
0
C
9
6
A
1
0
9
K
1
1
1
V
1
4
3
L
1
5
9
E
1
6
0
Y
1
6
1
C
1
6
2
S
1
6
3
R
1
6
5
H
1
6
9
F
2
1
2
[1]4i5m.a . T . . . . . . . . . . . . . . .
[1]4i5p.a . T . . . . . . . . . . . . . . .
[1]4i6b.a . T . . . . . . . . . . . . . . .
[1]4i6f.a . T . . . . . . . . . . . . . . .
[1]4i6h.a . T . . . . . . . . . . . . . . .

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
4i5m.a:r78
4i5p.a:1d1
4i6b.a:11g
4i6f.a:1c7
4i6h.a:1c8
[1] 4i5m.a
0
0 0 0 0
[1] 4i5p.a 0
0
0 0 0
[1] 4i6b.a 0.4 0.7
0
0.5 0.5
[1] 4i6f.a 0.2 0 0
0
0.1
[1] 4i6h.a 0.1 0 0 0
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
4i5m.a
4i5p.a
4i6b.a
4i6f.a
4i6h.a
[1] 4i5m.a
0
0 .04 .02 .01
[1] 4i5p.a 0
0
.04 .02 .01
[1] 4i6b.a .04 .04
0
.05 .04
[1] 4i6f.a .02 .02 .05
0
.02
[1] 4i6h.a .01 .01 .04 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
4i5m.a
4i5p.a
4i6b.a
4i6f.a
4i6h.a
[1] 4i5m.a
0
0.2 0.3 0.3 0.2
[1] 4i5p.a 0.2
0
0.2 0.3 0.3
[1] 4i6b.a 0.3 0.2
0
0.3 0.3
[1] 4i6f.a 0.3 0.3 0.3
0
0.3
[1] 4i6h.a 0.2 0.3 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
4i5m.a
4i5p.a
4i6b.a
4i6f.a
4i6h.a
[1] 4i5m.a
0
1.3 1.5 1.2 1.1
[1] 4i5p.a 1.3
0
0.8 0.6 0.6
[1] 4i6b.a 1.5 0.8
0
0.7 0.7
[1] 4i6f.a 1.2 0.6 0.7
0
0.4
[1] 4i6h.a 1.1 0.6 0.7 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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