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PLK4_HUMAN_1_277_ATPsite

Serine/threonine-protein kinase PLK4 [Protein kinase superfamily. Ser/Thr protein kinase family. CDC5/Polo subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PLK4_HUMAN):D: Protein kinase (18:24, 26, 28, 39, 41, 60, 73, 89:96, 99, 140:143, 153, 154, 160, 161, 164)18:24, 26, 28, 39, 41, 60, 73, 89:96, 99, 140:143, 153, 154, 160, 161, 164

Full PDB list

3cok, 4jxf, 4yur

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
1
8
G
1
9
K
2
0
G
2
1
F
2
3
V
2
6
R
2
8
A
3
9
K
4
1
L
7
3
L
8
9
E
9
0
M
9
1
C
9
2
H
9
3
N
9
4
G
9
5
E
9
6
R
9
9
S
1
4
0
L
1
4
2
L
1
4
3
A
1
5
3
D
1
5
4
Q
1
6
0
[1]3cok.a anp27 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4yur.a 4j743 . . . . . . . . . . . . . . . . . . . . . . . . -
[2]4jxf.a 63135 . . . . . . . . . . . . . . . . . . . . . . . . .

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
1
8
G
1
9
K
2
0
G
2
1
S
2
2
F
2
3
A
2
4
V
2
6
R
2
8
A
3
9
K
4
1
E
6
0
L
7
3
L
8
9
E
9
0
M
9
1
C
9
2
H
9
3
N
9
4
G
9
5
E
9
6
R
9
9
S
1
4
0
N
1
4
1
L
1
4
2
L
1
4
3
A
1
5
3
D
1
5
4
Q
1
6
0
L
1
6
1
P
1
6
4
[1]3cok.a . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . -
[1]4yur.a . . . . . . . . . . * . . . . . . . . . . . . . . . . . - - -
[2]4jxf.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
3cok.a:anp
4yur.a:4j7
4jxf.a:631
[1] 3cok.a
0.1
2.2 0.8
[1] 4yur.a 0
0
1.9
[2] 4jxf.a 4.9 6.5
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
3cok.a
4yur.a
4jxf.a
[1] 3cok.a
0
.11 .24
[1] 4yur.a .11
0
.32
[2] 4jxf.a .24 .32
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.1 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
3cok.a
4yur.a
4jxf.a
[1] 3cok.a
0
1.8 5.3
[1] 4yur.a 1.8
0
3.2
[2] 4jxf.a 5.3 3.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.7 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
3cok.a
4yur.a
4jxf.a
[1] 3cok.a
0
2.0 6.0
[1] 4yur.a 2.0
0
3.8
[2] 4jxf.a 6.0 3.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

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