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VRK2_HUMAN_12_335

Serine/threonine-protein kinase VRK2 [Protein kinase superfamily. CK1 Ser/Thr protein kinase family. VRK subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (VRK2_HUMAN):D: Protein kinase (35, 38, 43, 59, 61, 73, 77, 101, 119, 121:125, 170, 171, 173, 185, 186)35, 38, 43, 59, 61, 73, 77, 101, 119, 121:125, 170, 171, 173, 185, 186

Full PDB list

2v62, 5uu1

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
3
5
G
3
8
I
4
3
V
5
9
K
6
1
P
1
0
1
M
1
2
1
E
1
2
2
R
1
2
3
L
1
2
4
A
1
7
0
N
1
7
1
L
1
7
3
A
1
8
5
[1]2v62.b none . - . . . . . . . . . . . .
[1]5uu1.a 7dz28 . . . . . . . . . . . . . .

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
3
5
G
3
8
I
4
3
V
5
9
K
6
1
E
7
3
Y
7
7
P
1
0
1
M
1
1
9
M
1
2
1
E
1
2
2
R
1
2
3
L
1
2
4
G
1
2
5
A
1
7
0
N
1
7
1
L
1
7
3
A
1
8
5
D
1
8
6
[1]2v62.b . - . . . . . . . * . . . . . . . . .
[1]5uu1.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
2v62.b is apo
5uu1.a:7dz
[1] 2v62.b
-
2.1
[1] 5uu1.a -
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
2v62.b
5uu1.a
[1] 2v62.b
0
.11
[1] 5uu1.a .11
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
2v62.b
5uu1.a
[1] 2v62.b
0
0.8
[1] 5uu1.a 0.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
2v62.b
5uu1.a
[1] 2v62.b
0
1.1
[1] 5uu1.a 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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