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AUKBA_XENLA_78_360

Aurora kinase B-A [Protein kinase superfamily. Ser/Thr protein kinase family. Aurora subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AUKBA_XENLA):D: Protein kinase (97, 99:104, 107, 120, 122, 124, 138, 141, 142, 145, 154, 156, 168, 170:177, 180, 220, 221, 223, 233:235)97, 99:104, 107, 120, 122, 124, 138, 141, 142, 145, 154, 156, 168, 170:177, 180, 220, 221, 223, 233:235

Full PDB list

2bfx, 2bfy, 2vgo, 2vgp, 2vrx, 3ztx, 4b8l, 4b8m, 4c2v, 4c2w, 5eyk, 5k3y

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
R
9
7
L
9
9
G
1
0
0
K
1
0
1
G
1
0
2
K
1
0
3
F
1
0
4
V
1
0
7
A
1
2
0
K
1
2
2
L
1
3
8
E
1
4
1
I
1
4
2
Q
1
4
5
L
1
5
4
M
1
5
6
L
1
6
8
L
1
7
0
E
1
7
1
F
1
7
2
A
1
7
3
P
1
7
4
R
1
7
5
G
1
7
6
E
1
7
7
L
2
2
3
A
2
3
3
D
2
3
4
[1]2bfx.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2bfy.b h1n37 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2vgo.b ad529 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2vgp.a ad617 . . . . . - - . . . . . . . . . . . . . . . . . . . . .
[1]2vrx.a 44738 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3ztx.a ztx32 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4b8l.a a0p31 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4b8m.a vx633 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4c2v.a yja37 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4c2w.a anp31 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5eyk.a 5u535 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5k3y.a 6q440 . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
R
9
7
L
9
9
G
1
0
0
K
1
0
1
G
1
0
2
K
1
0
3
F
1
0
4
V
1
0
7
A
1
2
0
K
1
2
2
L
1
2
4
L
1
3
8
E
1
4
1
I
1
4
2
Q
1
4
5
L
1
5
4
M
1
5
6
L
1
6
8
L
1
7
0
E
1
7
1
F
1
7
2
A
1
7
3
P
1
7
4
R
1
7
5
G
1
7
6
E
1
7
7
K
1
8
0
E
2
2
0
N
2
2
1
L
2
2
3
A
2
3
3
D
2
3
4
F
2
3
5
[1]2bfx.a * . . . . . . . . * . . . . . . . . . . . . . . . * . . . . . . .
[1]2bfy.b . . . . . * . . . * . . . . . . . . . . . . . . . . . . . . . . .
[1]2vgo.b . . . . . * . . . * . . . . . . . . . . . . . . . . . . . . . . .
[1]2vgp.a * . . . . - - . . * . . . . . . . . . . . . . . . * . . . . . . .
[1]2vrx.a * . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . .
[1]3ztx.a . . . . . . . . . * . . . . . . . . . . . . . . . * . . . . . . .
[1]4b8l.a . . . . . * . . . * . . . . . . . . . . . . . . . . . . . . . . .
[1]4b8m.a * . . . . . . . . * . . . . . . . . . . . . . . . * . . . . . . .
[1]4c2v.a * . . . * * . . . * . . . . . . . . . . . . . . . * . . . . . . .
[1]4c2w.a * . . . . . . . . * . . . . . . . . . . . . . . . * . . . . . . .
[1]5eyk.a * . . . * * . . . * . . . . . . . . . . . . . . . . . . . . . . .
[1]5k3y.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
2bfx.a is apo
2bfy.b:h1n
2vgo.b:ad5
2vgp.a:ad6
2vrx.a:447
3ztx.a:ztx
4b8l.a:a0p
4b8m.a:vx6
4c2v.a:yja
4c2w.a:anp
5eyk.a:5u5
5k3y.a:6q4
[1] 2bfx.a
-
1.9 0.4 0 1.4 0.2 1.1 0.2 0.6 0.2 0.6 0.2
[1] 2bfy.b -
0.1
0.1 0 1.0 0 3.1 0 0.4 4.4 0.4 0.2
[1] 2vgo.b - 0.6
0
0 1.1 0.3 4.8 0 0.7 3.7 0.7 0.1
[1] 2vgp.a - 2.0 0.6
0
1.3 0.2 1.2 0.3 0.3 0.1 0.7 0.3
[1] 2vrx.a - 1.6 0.5 0
0
0.4 1.2 0.3 0.2 0.4 0.5 0.3
[1] 3ztx.a - 1.6 0.4 0 1.5
0.1
1.1 0.3 0.7 0.9 0.8 0.2
[1] 4b8l.a - 1.8 0.1 0 1.8 0.3
0
0.7 1.2 1.3 0.6 0.5
[1] 4b8m.a - 1.9 0.4 0 1.2 0.2 1.1
0
0.3 0.1 0.5 0.2
[1] 4c2v.a - 3.0 0.6 0 1.4 0.3 3.6 0.6
0
4.3 1.3 0.9
[1] 4c2w.a - 1.4 0.5 0 2.0 0.6 1.1 0.2 0.8
0.1
0.6 0.3
[1] 5eyk.a - 1.4 0.2 0 1.2 0.1 4.1 0 0.3 4.2
0
0.1
[1] 5k3y.a - 2.1 0.2 0 1.1 0 3.7 0.2 0.3 3.7 0.4
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
2bfx.a
2bfy.b
2vgo.b
2vgp.a
2vrx.a
3ztx.a
4b8l.a
4b8m.a
4c2v.a
4c2w.a
5eyk.a
5k3y.a
[1] 2bfx.a
0
.23 .24 .02 .07 .04 .14 .02 .17 .05 .19 .15
[1] 2bfy.b .23
0
.09 .23 .25 .20 .18 .23 .21 .24 .10 .13
[1] 2vgo.b .24 .09
0
.24 .24 .23 .20 .23 .22 .22 .12 .12
[1] 2vgp.a .02 .23 .24
0
.04 .05 .15 .01 .15 .07 .18 .14
[1] 2vrx.a .07 .25 .24 .04
0
.08 .18 .05 .17 .09 .20 .17
[1] 3ztx.a .04 .20 .23 .05 .08
0
.13 .04 .18 .08 .21 .18
[1] 4b8l.a .14 .18 .20 .15 .18 .13
0
.14 .22 .13 .18 .19
[1] 4b8m.a .02 .23 .23 .01 .05 .04 .14
0
.15 .06 .18 .14
[1] 4c2v.a .17 .21 .22 .15 .17 .18 .22 .15
0
.21 .13 .13
[1] 4c2w.a .05 .24 .22 .07 .09 .08 .13 .06 .21
0
.20 .18
[1] 5eyk.a .19 .10 .12 .18 .20 .21 .18 .18 .13 .20
0
.08
[1] 5k3y.a .15 .13 .12 .14 .17 .18 .19 .14 .13 .18 .08
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.3 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
2bfx.a
2bfy.b
2vgo.b
2vgp.a
2vrx.a
3ztx.a
4b8l.a
4b8m.a
4c2v.a
4c2w.a
5eyk.a
5k3y.a
[1] 2bfx.a
0
1.4 1.4 0.2 0.3 0.4 1.1 0.3 1.3 0.4 1.5 1.2
[1] 2bfy.b 1.4
0
0.4 0.9 1.3 1.4 1.2 1.4 1.2 1.2 0.4 0.7
[1] 2vgo.b 1.4 0.4
0
0.8 1.2 1.3 1.2 1.3 1.0 1.1 0.4 0.6
[1] 2vgp.a 0.2 0.9 0.8
0
0.2 0.3 0.9 0.2 1.0 0.3 0.9 0.7
[1] 2vrx.a 0.3 1.3 1.2 0.2
0
0.4 1.0 0.2 1.1 0.3 1.3 1.0
[1] 3ztx.a 0.4 1.4 1.3 0.3 0.4
0
1.0 0.3 1.2 0.5 1.4 1.0
[1] 4b8l.a 1.1 1.2 1.2 0.9 1.0 1.0
0
1.0 1.1 1.0 1.3 0.9
[1] 4b8m.a 0.3 1.4 1.3 0.2 0.2 0.3 1.0
0
1.2 0.4 1.4 1.1
[1] 4c2v.a 1.3 1.2 1.0 1.0 1.1 1.2 1.1 1.2
0
1.2 1.0 0.8
[1] 4c2w.a 0.4 1.2 1.1 0.3 0.3 0.5 1.0 0.4 1.2
0
1.3 1.0
[1] 5eyk.a 1.5 0.4 0.4 0.9 1.3 1.4 1.3 1.4 1.0 1.3
0
0.6
[1] 5k3y.a 1.2 0.7 0.6 0.7 1.0 1.0 0.9 1.1 0.8 1.0 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.0 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
2bfx.a
2bfy.b
2vgo.b
2vgp.a
2vrx.a
3ztx.a
4b8l.a
4b8m.a
4c2v.a
4c2w.a
5eyk.a
5k3y.a
[1] 2bfx.a
0
2.2 2.0 0.4 1.3 0.9 1.7 0.9 1.9 1.1 2.0 1.9
[1] 2bfy.b 2.2
0
1.1 1.3 1.9 1.8 1.5 1.8 1.3 1.7 0.9 1.0
[1] 2vgo.b 2.0 1.1
0
1.1 1.8 1.7 1.5 1.7 1.1 1.6 0.8 1.0
[1] 2vgp.a 0.4 1.3 1.1
0
1.0 0.6 1.2 0.7 1.1 0.6 1.0 1.0
[1] 2vrx.a 1.3 1.9 1.8 1.0
0
1.3 1.5 1.0 1.6 1.1 1.7 1.6
[1] 3ztx.a 0.9 1.8 1.7 0.6 1.3
0
1.4 0.8 1.6 0.9 1.7 1.5
[1] 4b8l.a 1.7 1.5 1.5 1.2 1.5 1.4
0
1.4 1.5 1.4 1.4 1.3
[1] 4b8m.a 0.9 1.8 1.7 0.7 1.0 0.8 1.4
0
1.5 0.9 1.6 1.4
[1] 4c2v.a 1.9 1.3 1.1 1.1 1.6 1.6 1.5 1.5
0
1.6 1.1 1.0
[1] 4c2w.a 1.1 1.7 1.6 0.6 1.1 0.9 1.4 0.9 1.6
0
1.4 1.5
[1] 5eyk.a 2.0 0.9 0.8 1.0 1.7 1.7 1.4 1.6 1.1 1.4
0
1.0
[1] 5k3y.a 1.9 1.0 1.0 1.0 1.6 1.5 1.3 1.4 1.0 1.5 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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