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ABL2_HUMAN_275_551

Abelson tyrosine-protein kinase 2 [Protein kinase superfamily. Tyr protein kinase family. ABL subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ABL2_HUMAN):D: Protein kinase (294, 295, 298, 299, 302, 315:317, 332, 335, 336, 339, 345, 359, 361:367, 405:408, 414, 416, 426:432)294, 295, 298, 299, 302, 315:317, 332, 335, 336, 339, 345, 359, 361:367, 405:408, 414, 416, 426:432

Full PDB list

2xyn, 3gvu, 3hmi, 4xli

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
2
9
4
G
2
9
5
Q
2
9
8
Y
2
9
9
V
3
0
2
A
3
1
5
V
3
1
6
K
3
1
7
E
3
3
2
V
3
3
5
M
3
3
6
I
3
3
9
V
3
4
5
I
3
5
9
T
3
6
1
E
3
6
2
Y
3
6
3
M
3
6
4
P
3
6
5
Y
3
6
6
G
3
6
7
I
4
0
6
H
4
0
7
N
4
1
4
L
4
1
6
A
4
2
6
D
4
2
7
F
4
2
8
[1]2xyn.a vx633 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4xli.b 1n133 . . - - . . . . . . . . . . . . . . . . . . . . . . . .
[2]3gvu.a sti37 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[3]3hmi.a dki28 . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
L
2
9
4
G
2
9
5
Q
2
9
8
Y
2
9
9
V
3
0
2
A
3
1
5
V
3
1
6
K
3
1
7
E
3
3
2
V
3
3
5
M
3
3
6
I
3
3
9
V
3
4
5
I
3
5
9
T
3
6
1
E
3
6
2
Y
3
6
3
M
3
6
4
P
3
6
5
Y
3
6
6
G
3
6
7
F
4
0
5
I
4
0
6
H
4
0
7
R
4
0
8
N
4
1
4
L
4
1
6
A
4
2
6
D
4
2
7
F
4
2
8
G
4
2
9
L
4
3
0
S
4
3
1
R
4
3
2
[1]2xyn.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * . * * .
[1]4xli.b . . - - . . . . . . . . . . . . . . . . . . . . . . . . * * . * * .
[2]3gvu.a . . . * . . . . . . . . . . . . . . . . . . . . . . . . . * . . . .
[3]3hmi.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
2xyn.a:vx6
4xli.b:1n1
3gvu.a:sti
3hmi.a:dki
[1] 2xyn.a
0.1
0.2 8.8 1.8
[1] 4xli.b 0.2
0
9.3 1.8
[2] 3gvu.a 3.0 1.7
0
5.9
[3] 3hmi.a 4.8 4.2 14
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (3 clusters)

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
2xyn.a
4xli.b
3gvu.a
3hmi.a
[1] 2xyn.a
0
.03 .27 .32
[1] 4xli.b .03
0
.28 .33
[2] 3gvu.a .27 .28
0
.35
[3] 3hmi.a .32 .33 .35
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 3.1 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
2xyn.a
4xli.b
3gvu.a
3hmi.a
[1] 2xyn.a
0
0.8 4.9 1.9
[1] 4xli.b 0.8
0
5.0 1.9
[2] 3gvu.a 4.9 5.0
0
5.5
[3] 3hmi.a 1.9 1.9 5.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.9 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
2xyn.a
4xli.b
3gvu.a
3hmi.a
[1] 2xyn.a
0
0.9 4.5 3.0
[1] 4xli.b 0.9
0
4.5 3.1
[2] 3gvu.a 4.5 4.5
0
5.0
[3] 3hmi.a 3.0 3.1 5.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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