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DYR1A_HUMAN_124_488_ATP

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 (165:168, 170:173, 186, 188, 203, 222, 238:244, 246, 289, 291, 292, 294, 306, 307)165:168, 170:173, 186, 188, 203, 222, 238:244, 246, 289, 291, 292, 294, 306, 307

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

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
1
6
5
G
1
6
6
K
1
6
7
G
1
6
8
F
1
7
0
G
1
7
1
Q
1
7
2
V
1
7
3
A
1
8
6
K
1
8
8
E
2
0
3
V
2
2
2
F
2
3
8
E
2
3
9
M
2
4
0
L
2
4
1
S
2
4
2
Y
2
4
3
N
2
4
4
E
2
9
1
N
2
9
2
L
2
9
4
V
3
0
6
D
3
0
7
[1]2vx3.c d1532 . . . . . . . . . . . . . . . . . . . . . . . .
[1]3anq.b ehb16 . . . . . . . . . . . . . . . . . . . . . . . .
[1]3anr.a hrm16 . . . . . . . . . . . . . . . . . . . . . . . .
[1]4aze.a 3ra23 . . . . . . . . . . . . . . . . . . . . . . . .
[1]4mq1.a 2c337 . . . . . . . . . . . . . . . . . . . . . . . .
[1]4mq2.c 2c427 . . . . . . . . . . . . . . . . . . . . . . . .
[1]4nct.a 2k243 . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ylj.c 4e121 . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ylk.a 4e222 . . . . . . . . . . . . . . . . . . . . . . . .
[1]4yll.a 4e322 . . . . . . . . . . . . . . . . . . . . . . . .
[1]4yu2.a 4h519 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5a3x.a qiv14 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5a4e.c 7qq15 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5a4l.c zc314 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5a4q.a y3l14 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5a4t.c ajg15 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5a54.a 5pw16 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5aik.a awr24 . . . . . . . . . . . . . . . . . . . . . . . .

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
1
6
5
G
1
6
6
K
1
6
7
G
1
6
8
F
1
7
0
G
1
7
1
Q
1
7
2
V
1
7
3
A
1
8
6
K
1
8
8
E
2
0
3
V
2
2
2
F
2
3
8
E
2
3
9
M
2
4
0
L
2
4
1
S
2
4
2
Y
2
4
3
N
2
4
4
Y
2
4
6
K
2
8
9
E
2
9
1
N
2
9
2
L
2
9
4
V
3
0
6
D
3
0
7
[1]2vx3.c . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3anq.b . . . . * . . . . . . . . . . . . . . . . . . . . .
[1]3anr.a . . . . * . . . . . . . . . . . . . . . . . . . . .
[1]4aze.a . . . . * . . . . . . . . . . . . . . . . . . . . .
[1]4mq1.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4mq2.c . . . . * . . . . . . . . . . . . . . . . . . . . .
[1]4nct.a . . . . * . . . . . . . . . . * . . . . . . . . . .
[1]4ylj.c * . . . * . . . . . . . . . . . . . . . . . . . . .
[1]4ylk.a . . . . * . . . . . . . . . . * . . . . . . . . . .
[1]4yll.a . . . . * . . . . . . . . . . * . . . . . . . . . .
[1]4yu2.a . . . . * . . . . . . . . . . . . . . . . . . . . .
[1]5a3x.a . . . . * . . . . . . . . . . * . . . . . . . . . .
[1]5a4e.c . . . . * . . . . . . . . . . * . . . . . . . . . .
[1]5a4l.c . . . . * . . . . . . . . . . * . . . . . . . . . .
[1]5a4q.a . . . . * . . . . . . . . . . * . . . . . . . . . .
[1]5a4t.c . . . . * . . . . . . . . . . . . . . . . . . . . .
[1]5a54.a . . . . * . . . . . . . . . . * . . . . . . . . . .
[1]5aik.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
2vx3.c:d15
3anq.b:ehb
3anr.a:hrm
4aze.a:3ra
4mq1.a:2c3
4mq2.c:2c4
4nct.a:2k2
4ylj.c:4e1
4ylk.a:4e2
4yll.a:4e3
4yu2.a:4h5
5a3x.a:qiv
5a4e.c:7qq
5a4l.c:zc3
5a4q.a:y3l
5a4t.c:ajg
5a54.a:5pw
5aik.a:awr
[1] 2vx3.c
0.1
0 0.1 0 0.7 0.1 0.3 0 0 0.1 0 0 0 0 0 0 0 0
[1] 3anq.b 2.8
0
0 0.1 3.9 0.2 0.7 0.1 0.1 0.3 0 0 0.1 0 0 0 0 0
[1] 3anr.a 2.9 0.2
0
0.1 3.5 0.2 0.4 0 0.2 0.3 0 0.3 0 0.2 0 0 0 0.1
[1] 4aze.a 3.6 0.2 0.1
0
3.9 0.2 1.2 0.1 0.4 0.4 0 0.5 0.2 0.2 0.2 0.1 0.2 0.3
[1] 4mq1.a 0.2 0.5 0.2 0.2
0
0 1.0 0.2 0.3 0.5 0.1 0.6 0.1 0.3 0.1 0.1 0.1 0.4
[1] 4mq2.c 3.6 0.2 0 0 4.7
0.1
1.4 0.4 0.3 0.4 0 0.5 0.1 0 0 0 0 0.4
[1] 4nct.a 1.9 0.1 0 0.1 3.1 0.5
0
0.2 0.1 0.2 0.1 0 0 0.1 0 0.1 0 0
[1] 4ylj.c 2.6 0.3 0.1 0 3.5 0.2 1.5
0
0.1 0.1 0 0.6 0.1 0.2 0.3 0.1 0.3 0.3
[1] 4ylk.a 4.6 0.2 0.2 0.4 5.6 1.3 1.5 0.8
0
0 0.4 0.6 0.1 0.1 0.1 0.4 0.1 0.6
[1] 4yll.a 4.6 0.3 0.3 0.4 5.8 1.3 1.7 0.8 0
0
0.3 0.8 0.1 0.1 0.1 0.4 0.1 0.6
[1] 4yu2.a 3.4 0.3 0 0 4.7 0.1 1.2 0.2 0.2 0.3
0
0.8 0.1 0.3 0 0 0 0.6
[1] 5a3x.a 3.1 0 0 0.1 4.1 0.6 0.7 0.2 0.4 0.4 0.1
0
0.1 0 0.1 0.2 0.1 0
[1] 5a4e.c 2.6 0.1 0.2 0.1 3.7 0.3 1.8 0.2 0.2 0.2 0.2 0.3
0
0.1 0 0.1 0 0.3
[1] 5a4l.c 3.3 0 0.1 0.1 4.1 0.5 1.3 0.1 0.3 0.3 0.3 0.1 0.1
0
0.2 0.2 0.1 0.2
[1] 5a4q.a 2.7 0 0 0.1 4.0 0.6 0.2 0.2 0 0.1 0.1 0 0 0
0
0.1 0 0
[1] 5a4t.c 2.7 0.1 0.1 0.1 3.6 0.4 0.6 0.2 0.1 0.1 0.2 0.3 0.1 0.1 0
0
0.1 0.1
[1] 5a54.a 3.2 0.1 0.1 0.2 4.3 0.5 0.6 0.1 0.1 0.1 0.1 0.2 0.1 0.1 0 0.1
0
0.1
[1] 5aik.a 2.4 0 0 0.1 3.9 0.4 0.1 0 0.1 0.1 0 0 0 0 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

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

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
2vx3.c
3anq.b
3anr.a
4aze.a
4mq1.a
4mq2.c
4nct.a
4ylj.c
4ylk.a
4yll.a
4yu2.a
5a3x.a
5a4e.c
5a4l.c
5a4q.a
5a4t.c
5a54.a
5aik.a
[1] 2vx3.c
0
.16 .14 .18 .08 .21 .13 .17 .25 .26 .19 .17 .18 .19 .16 .15 .17 .15
[1] 3anq.b .16
0
.03 .06 .19 .10 .06 .07 .14 .15 .08 .03 .07 .06 .04 .05 .05 .05
[1] 3anr.a .14 .03
0
.08 .18 .11 .04 .08 .14 .15 .07 .03 .07 .08 .03 .05 .05 .05
[1] 4aze.a .18 .06 .08
0
.19 .06 .11 .05 .14 .15 .04 .08 .09 .08 .10 .08 .07 .09
[1] 4mq1.a .08 .19 .18 .19
0
.22 .17 .17 .27 .28 .22 .20 .21 .22 .20 .20 .22 .20
[1] 4mq2.c .21 .10 .11 .06 .22
0
.14 .08 .13 .14 .05 .10 .12 .10 .12 .10 .08 .12
[1] 4nct.a .13 .06 .04 .11 .17 .14
0
.12 .16 .17 .10 .07 .09 .11 .04 .08 .08 .05
[1] 4ylj.c .17 .07 .08 .05 .17 .08 .12
0
.15 .16 .08 .08 .08 .05 .11 .07 .08 .07
[1] 4ylk.a .25 .14 .14 .14 .27 .13 .16 .15
0
.01 .11 .13 .16 .15 .13 .15 .12 .12
[1] 4yll.a .26 .15 .15 .15 .28 .14 .17 .16 .01
0
.12 .14 .17 .15 .14 .16 .13 .13
[1] 4yu2.a .19 .08 .07 .04 .22 .05 .10 .08 .11 .12
0
.09 .12 .10 .09 .08 .06 .08
[1] 5a3x.a .17 .03 .03 .08 .20 .10 .07 .08 .13 .14 .09
0
.06 .05 .04 .04 .06 .05
[1] 5a4e.c .18 .07 .07 .09 .21 .12 .09 .08 .16 .17 .12 .06
0
.04 .08 .06 .08 .10
[1] 5a4l.c .19 .06 .08 .08 .22 .10 .11 .05 .15 .15 .10 .05 .04
0
.09 .05 .06 .07
[1] 5a4q.a .16 .04 .03 .10 .20 .12 .04 .11 .13 .14 .09 .04 .08 .09
0
.07 .05 .04
[1] 5a4t.c .15 .05 .05 .08 .20 .10 .08 .07 .15 .16 .08 .04 .06 .05 .07
0
.07 .06
[1] 5a54.a .17 .05 .05 .07 .22 .08 .08 .08 .12 .13 .06 .06 .08 .06 .05 .07
0
.05
[1] 5aik.a .15 .05 .05 .09 .20 .12 .05 .07 .12 .13 .08 .05 .10 .07 .04 .06 .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
2vx3.c
3anq.b
3anr.a
4aze.a
4mq1.a
4mq2.c
4nct.a
4ylj.c
4ylk.a
4yll.a
4yu2.a
5a3x.a
5a4e.c
5a4l.c
5a4q.a
5a4t.c
5a54.a
5aik.a
[1] 2vx3.c
0
0.7 0.6 0.4 0.4 0.5 1.0 0.4 0.7 0.8 0.5 0.6 0.5 0.6 0.7 0.6 0.7 0.7
[1] 3anq.b 0.7
0
0.2 0.7 0.8 0.7 0.6 0.6 1.0 1.0 0.7 0.3 0.6 0.5 0.3 0.4 0.3 0.4
[1] 3anr.a 0.6 0.2
0
0.6 0.7 0.6 0.7 0.5 0.9 0.9 0.6 0.2 0.5 0.4 0.3 0.4 0.3 0.4
[1] 4aze.a 0.4 0.7 0.6
0
0.5 0.4 1.1 0.4 1.0 1.0 0.4 0.7 0.5 0.6 0.8 0.7 0.7 0.9
[1] 4mq1.a 0.4 0.8 0.7 0.5
0
0.6 1.1 0.4 0.9 1.0 0.6 0.8 0.7 0.7 0.8 0.7 0.8 0.8
[1] 4mq2.c 0.5 0.7 0.6 0.4 0.6
0
1.1 0.4 0.9 0.9 0.2 0.6 0.4 0.6 0.7 0.7 0.6 0.8
[1] 4nct.a 1.0 0.6 0.7 1.1 1.1 1.1
0
0.9 1.4 1.4 1.1 0.7 0.9 0.8 0.4 0.5 0.6 0.5
[1] 4ylj.c 0.4 0.6 0.5 0.4 0.4 0.4 0.9
0
1.0 1.0 0.4 0.6 0.5 0.6 0.7 0.6 0.6 0.7
[1] 4ylk.a 0.7 1.0 0.9 1.0 0.9 0.9 1.4 1.0
0
0.1 0.9 0.9 0.9 1.0 1.0 1.0 1.0 1.0
[1] 4yll.a 0.8 1.0 0.9 1.0 1.0 0.9 1.4 1.0 0.1
0
0.9 0.9 0.9 1.0 1.0 1.0 1.0 1.0
[1] 4yu2.a 0.5 0.7 0.6 0.4 0.6 0.2 1.1 0.4 0.9 0.9
0
0.6 0.5 0.7 0.7 0.7 0.7 0.8
[1] 5a3x.a 0.6 0.3 0.2 0.7 0.8 0.6 0.7 0.6 0.9 0.9 0.6
0
0.4 0.4 0.4 0.4 0.3 0.5
[1] 5a4e.c 0.5 0.6 0.5 0.5 0.7 0.4 0.9 0.5 0.9 0.9 0.5 0.4
0
0.4 0.7 0.6 0.6 0.7
[1] 5a4l.c 0.6 0.5 0.4 0.6 0.7 0.6 0.8 0.6 1.0 1.0 0.7 0.4 0.4
0
0.6 0.4 0.5 0.6
[1] 5a4q.a 0.7 0.3 0.3 0.8 0.8 0.7 0.4 0.7 1.0 1.0 0.7 0.4 0.7 0.6
0
0.4 0.3 0.3
[1] 5a4t.c 0.6 0.4 0.4 0.7 0.7 0.7 0.5 0.6 1.0 1.0 0.7 0.4 0.6 0.4 0.4
0
0.4 0.4
[1] 5a54.a 0.7 0.3 0.3 0.7 0.8 0.6 0.6 0.6 1.0 1.0 0.7 0.3 0.6 0.5 0.3 0.4
0
0.4
[1] 5aik.a 0.7 0.4 0.4 0.9 0.8 0.8 0.5 0.7 1.0 1.0 0.8 0.5 0.7 0.6 0.3 0.4 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
2vx3.c
3anq.b
3anr.a
4aze.a
4mq1.a
4mq2.c
4nct.a
4ylj.c
4ylk.a
4yll.a
4yu2.a
5a3x.a
5a4e.c
5a4l.c
5a4q.a
5a4t.c
5a54.a
5aik.a
[1] 2vx3.c
0
1.2 1.2 1.2 1.0 1.2 1.4 1.2 1.7 1.7 1.3 1.3 1.3 1.5 1.3 1.5 1.5 1.4
[1] 3anq.b 1.2
0
0.3 0.8 1.4 0.8 0.7 0.8 1.3 1.3 0.8 0.5 0.9 0.9 0.5 0.9 0.9 0.6
[1] 3anr.a 1.2 0.3
0
0.8 1.4 0.8 0.8 0.7 1.2 1.3 0.7 0.5 0.9 0.9 0.6 0.9 0.9 0.6
[1] 4aze.a 1.2 0.8 0.8
0
1.4 0.6 1.1 0.5 1.4 1.4 0.5 0.8 0.9 0.9 0.9 1.0 1.1 1.0
[1] 4mq1.a 1.0 1.4 1.4 1.4
0
1.5 1.6 1.3 1.8 1.8 1.4 1.5 1.6 1.4 1.5 1.4 1.4 1.4
[1] 4mq2.c 1.2 0.8 0.8 0.6 1.5
0
1.1 0.6 1.3 1.4 0.5 0.8 0.9 1.0 0.9 1.1 1.1 1.0
[1] 4nct.a 1.4 0.7 0.8 1.1 1.6 1.1
0
1.0 1.7 1.8 1.1 0.7 1.1 1.1 0.6 0.9 0.9 0.7
[1] 4ylj.c 1.2 0.8 0.7 0.5 1.3 0.6 1.0
0
1.5 1.5 0.5 0.8 0.9 1.0 0.8 1.0 1.1 0.9
[1] 4ylk.a 1.7 1.3 1.2 1.4 1.8 1.3 1.7 1.5
0
0.3 1.3 1.4 1.5 1.4 1.4 1.5 1.4 1.2
[1] 4yll.a 1.7 1.3 1.3 1.4 1.8 1.4 1.8 1.5 0.3
0
1.4 1.4 1.5 1.4 1.5 1.5 1.4 1.3
[1] 4yu2.a 1.3 0.8 0.7 0.5 1.4 0.5 1.1 0.5 1.3 1.4
0
0.8 0.9 1.0 0.9 1.0 1.0 0.9
[1] 5a3x.a 1.3 0.5 0.5 0.8 1.5 0.8 0.7 0.8 1.4 1.4 0.8
0
0.8 0.8 0.6 0.8 0.8 0.7
[1] 5a4e.c 1.3 0.9 0.9 0.9 1.6 0.9 1.1 0.9 1.5 1.5 0.9 0.8
0
0.9 0.8 1.0 1.1 1.1
[1] 5a4l.c 1.5 0.9 0.9 0.9 1.4 1.0 1.1 1.0 1.4 1.4 1.0 0.8 0.9
0
0.8 0.5 0.7 0.8
[1] 5a4q.a 1.3 0.5 0.6 0.9 1.5 0.9 0.6 0.8 1.4 1.5 0.9 0.6 0.8 0.8
0
0.8 0.8 0.6
[1] 5a4t.c 1.5 0.9 0.9 1.0 1.4 1.1 0.9 1.0 1.5 1.5 1.0 0.8 1.0 0.5 0.8
0
0.6 0.8
[1] 5a54.a 1.5 0.9 0.9 1.1 1.4 1.1 0.9 1.1 1.4 1.4 1.0 0.8 1.1 0.7 0.8 0.6
0
0.8
[1] 5aik.a 1.4 0.6 0.6 1.0 1.4 1.0 0.7 0.9 1.2 1.3 0.9 0.7 1.1 0.8 0.6 0.8 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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