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DYR1A_HUMAN_124_488_pep

Dual specificity tyrosine-phosphorylation-regulated kinase 1A [Protein kinase superfamily. CMGC Ser/Thr protein kinase family. MNB/DYRK subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DYR1A_HUMAN):D: Protein kinase (169, 170, 195, 196, 199, 246, 287, 289:291, 310, 319, 321:328, 353, 359)169, 170, 195, 196, 199, 246, 287, 289:291, 310, 319, 321:328, 353, 359
Cofactors (cF):4h5

Full PDB list

2vx3, 2wo6, 3anq, 3anr, 4aze, 4mq1, 4mq2, 4nct, 4ylj, 4ylk, 4yll, 4yu2, 5a3x, 5a4e, 5a4l, 5a4q, 5a4t, 5a54, 5aik (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 cF
F
1
7
0
A
1
9
5
F
1
9
6
Y
2
4
6
D
2
8
7
K
2
8
9
P
2
9
0
E
2
9
1
S
3
1
0
Y
3
1
9
Y
3
2
1
I
3
2
2
Q
3
2
3
S
3
2
4
R
3
2
5
F
3
2
6
Y
3
2
7
R
3
2
8
E
3
5
3
[1]2vx3.a p6g7 . . . . . . . . . . * . . . . . . . .
[1]2wo6.b ARPGTPAL54 . . . . . . . . . . * . . . . . . . .
[1]4ylj.a pg410 . . . . . . . . . . * . . . . . . . .
[1]4yu2.b none . . . . . . . . . . * . . . . . . . . 4h5

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

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PDB.ch
A1 cF
S
1
6
9
F
1
7
0
A
1
9
5
F
1
9
6
Q
1
9
9
Y
2
4
6
D
2
8
7
K
2
8
9
P
2
9
0
E
2
9
1
S
3
1
0
Y
3
1
9
Y
3
2
1
I
3
2
2
Q
3
2
3
S
3
2
4
R
3
2
5
F
3
2
6
Y
3
2
7
R
3
2
8
E
3
5
3
P
3
5
9
[1]2vx3.a . . . . . . . . . . . . * . . . . . . . . .
[1]2wo6.b . . . . . . . . . . . . * . . . . . . . . .
[1]4ylj.a . . . . . . . . . . . . * . . . . . . . . .
[1]4yu2.b . . . . . . . . . . . . * . . . . . . . . . 4h5

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
2vx3.a:p6g
2wo6.b:ARPGTPAL
4ylj.a:pg4
4yu2.b is apo
[1] 2vx3.a
0
0.3 0 -
[1] 2wo6.b 0.1
0
0.1 -
[1] 4ylj.a 0 0.3
0
-
[1] 4yu2.b 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
2vx3.a
2wo6.b
4ylj.a
4yu2.b
[1] 2vx3.a
0
.02 .01 .01
[1] 2wo6.b .02
0
.02 0
[1] 4ylj.a .01 .02
0
.01
[1] 4yu2.b .01 0 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.1 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
2vx3.a
2wo6.b
4ylj.a
4yu2.b
[1] 2vx3.a
0
0.4 0.3 0.4
[1] 2wo6.b 0.4
0
0.5 0.6
[1] 4ylj.a 0.3 0.5
0
0.3
[1] 4yu2.b 0.4 0.6 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
2vx3.a
2wo6.b
4ylj.a
4yu2.b
[1] 2vx3.a
0
0.7 1.1 1.6
[1] 2wo6.b 0.7
0
1.3 1.6
[1] 4ylj.a 1.1 1.3
0
1.2
[1] 4yu2.b 1.6 1.6 1.2
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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