If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

DYRK2_HUMAN_145_550

Dual specificity tyrosine-phosphorylation-regulated kinase 2 [Protein kinase superfamily. CMGC Ser/Thr protein kinase family. MNB/DYRK subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DYRK2_HUMAN):D: Protein kinase (228:230, 233, 236, 249, 251, 266, 285, 301:307, 352, 353, 355, 367, 368)228:230, 233, 236, 249, 251, 266, 285, 301:307, 352, 353, 355, 367, 368

Full PDB list

3k2l, 3kvw, 4azf, 5lxc, 5lxd

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
2
2
8
G
2
2
9
K
2
3
0
F
2
3
3
V
2
3
6
A
2
4
9
K
2
5
1
I
2
8
5
F
3
0
1
E
3
0
2
L
3
0
3
L
3
0
4
S
3
0
5
M
3
0
6
N
3
0
7
E
3
5
2
L
3
5
5
I
3
6
7
D
3
6
8
[1]3k2l.a none . . . . . . . . . . . . . . . . . . .
[1]3kvw.a irb25 . . . . . . . . . . . . . . . . . . .
[1]4azf.a 3ra23 . . . . . . . . . . . . . . . . . . .
[1]5lxc.a 7aa26 . . . . . . . . . . . . . . . . . . .
[1]5lxd.a 7a727 . . . . . . . . . . . . . . . . . . .

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
2
2
8
G
2
2
9
K
2
3
0
F
2
3
3
V
2
3
6
A
2
4
9
K
2
5
1
E
2
6
6
I
2
8
5
F
3
0
1
E
3
0
2
L
3
0
3
L
3
0
4
S
3
0
5
M
3
0
6
N
3
0
7
E
3
5
2
N
3
5
3
L
3
5
5
I
3
6
7
D
3
6
8
[1]3k2l.a . . . . . . . . . . . . . . . . . . . . .
[1]3kvw.a . . . . . . . . . . . . . . . . . . . . .
[1]4azf.a . . . . . . . . . . . . . . . . . . . . .
[1]5lxc.a . . . . . . . . . . . . . . . . . . . . .
[1]5lxd.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

zoom: [−] [+]; [view as image]; [download as text]

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
3k2l.a is apo
3kvw.a:irb
4azf.a:3ra
5lxc.a:7aa
5lxd.a:7a7
[1] 3k2l.a
-
0 0.1 0.3 0.1
[1] 3kvw.a -
0
0 0.1 0.1
[1] 4azf.a - 0.1
0
0 0
[1] 5lxc.a - 0.6 0.3
0
0.1
[1] 5lxd.a - 0.6 0.2 0.3
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
3k2l.a
3kvw.a
4azf.a
5lxc.a
5lxd.a
[1] 3k2l.a
0
.02 .02 .06 .04
[1] 3kvw.a .02
0
.01 .04 .04
[1] 4azf.a .02 .01
0
.05 .03
[1] 5lxc.a .06 .04 .05
0
.04
[1] 5lxd.a .04 .04 .03 .04
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

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
3k2l.a
3kvw.a
4azf.a
5lxc.a
5lxd.a
[1] 3k2l.a
0
0.3 0.3 0.7 0.4
[1] 3kvw.a 0.3
0
0.2 0.7 0.4
[1] 4azf.a 0.3 0.2
0
0.6 0.4
[1] 5lxc.a 0.7 0.7 0.6
0
0.6
[1] 5lxd.a 0.4 0.4 0.4 0.6
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
3k2l.a
3kvw.a
4azf.a
5lxc.a
5lxd.a
[1] 3k2l.a
0
0.5 0.4 0.8 0.7
[1] 3kvw.a 0.5
0
0.5 0.9 0.7
[1] 4azf.a 0.4 0.5
0
0.8 0.7
[1] 5lxc.a 0.8 0.9 0.8
0
0.6
[1] 5lxd.a 0.7 0.7 0.7 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

loading...