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ABL1_HUMAN_228_509_allosteric

Tyrosine-protein kinase ABL1 [Protein kinase superfamily. Tyr protein kinase family. ABL subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ABL1_HUMAN):D: Protein kinase (332, 336:338, 340, 341, 344, 429, 432:435, 437, 462:465, 468, 493)
496, 497, 499:506, 510
332, 336:338, 340, 341, 344, 429, 432:435, 437, 462:465, 468, 493, 496, 497, 499:506, 510

Full PDB list

1fpu, 1iep, 1m52, 1opj, 1opk, 1opl, 2e2b, 2f4j, 2fo0, 2g1t, 2g2f, 2g2h, 2g2i, 2gqg, 2hiw, 2hyy, 2hz0, 2hz4, 2hzi, 2hzn, 2qoh, 2v7a, 2z60, 3cs9, 3dk3, 3dk6, 3dk7, 3ik3, 3k5v, 3kf4, 3kfa, 3ms9, 3mss, 3oxz, 3oy3, 3pyy, 3qri, 3qrj, 3qrk, 3ue4, 4twp, 4wa9, 4xey, 4yc8, 4zog, 5hu9, 5mo4 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
R
3
3
2
A
3
3
7
V
3
3
8
L
3
4
0
L
3
4
1
A
3
4
4
L
4
2
9
I
4
3
2
A
4
3
3
T
4
3
4
Y
4
3
5
E
4
6
2
G
4
6
3
C
4
6
4
P
4
6
5
V
4
6
8
F
4
9
3
M
4
9
6
I
5
0
2
V
5
0
6
L
5
1
0
[1]2qoh.b none . . . . . . . . . . . . . . . . . . . . .
[1]3ms9.a ms912 . . . . . . . . . . . . . . . . . . - - -
[1]3mss.c ms721 . . . . . . . . . . . . . . . . . . - - -
[1]3pyy.a 3yy25 . . . . . . . . . . . . . . . . . . - - -
[1]4zog.b none . . . . . . . . . . . . . . . . . . . - -
[2]1opj.b myr15 . . . . . . . . . . . . . . . . . . . . .
[2]2fo0.a myr15 . . . . . . . . . . . . . . . . . . . . .
[2]3k5v.a stj27 . . . . . . . . . . . . . . . . . . . . .
[2]5mo4.a ay731 . . . . . . . . . . . . . . . . . . . . .

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
R
3
3
2
N
3
3
6
A
3
3
7
V
3
3
8
L
3
4
0
L
3
4
1
A
3
4
4
L
4
2
9
I
4
3
2
A
4
3
3
T
4
3
4
Y
4
3
5
M
4
3
7
E
4
6
2
G
4
6
3
C
4
6
4
P
4
6
5
V
4
6
8
F
4
9
3
M
4
9
6
F
4
9
7
E
4
9
9
S
5
0
0
S
5
0
1
I
5
0
2
S
5
0
3
D
5
0
4
E
5
0
5
V
5
0
6
L
5
1
0
[1]2qoh.b . S . . . . . . . . . . . . . . . . . . . . * . . . . . . .
[1]3ms9.a . S . . . . . . . . . . . . . . . . . . . - - - - - - - - -
[1]3mss.c . S . . . . . . . . . . . . . . . . . . . - - - - - - - - -
[1]3pyy.a . . . . . . . . . . . . . . . . . . . . . . * - - - - - - -
[1]4zog.b . . . . . . . . . . . . . . . . . . . . . . . . . . - - - -
[2]1opj.b . S . . . . . . . . . . . . . . . . . . * . . * * . . . * .
[2]2fo0.a . . . . . . . . . . . . . . . . . . . . * . * * * . . . * .
[2]3k5v.a . S . . . . . . . . . . . . . . . . . . * . * * * . . . * .
[2]5mo4.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
2qoh.b is apo
3ms9.a:ms9
3mss.c:ms7
3pyy.a:3yy
4zog.b is apo
1opj.b:myr
2fo0.a:myr
3k5v.a:stj
5mo4.a:ay7
[1] 2qoh.b
-
0.3 1.4 0.3 - 0.3 0 0.3 0.9
[1] 3ms9.a -
0
0 0.5 - 0.1 0.1 0.2 0.4
[1] 3mss.c - 0
0
0.6 - 0.1 0.1 0.1 0.2
[1] 3pyy.a - 0.3 1.4
0
- 0.1 0 0.1 0.1
[1] 4zog.b - 0.1 0.8 0.6
-
0.3 0.2 0.2 0.6
[2] 1opj.b - 2.6 9.9 4.7 -
0
0 0.1 0.2
[2] 2fo0.a - 2.6 9.9 4.5 - 0
0
0 0.6
[2] 3k5v.a - 2.6 10 4.3 - 0 0
0
0.1
[2] 5mo4.a - 2.7 9.3 4.3 - 0 0 0
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 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
2qoh.b
3ms9.a
3mss.c
3pyy.a
4zog.b
1opj.b
2fo0.a
3k5v.a
5mo4.a
[1] 2qoh.b
0
.06 .07 .05 .05 .40 .39 .38 .36
[1] 3ms9.a .06
0
.01 .07 .04 .38 .38 .37 .35
[1] 3mss.c .07 .01
0
.07 .04 .37 .38 .37 .35
[1] 3pyy.a .05 .07 .07
0
.06 .38 .37 .36 .33
[1] 4zog.b .05 .04 .04 .06
0
.38 .37 .37 .34
[2] 1opj.b .40 .38 .37 .38 .38
0
.07 .05 .11
[2] 2fo0.a .39 .38 .38 .37 .37 .07
0
.05 .07
[2] 3k5v.a .38 .37 .37 .36 .37 .05 .05
0
.08
[2] 5mo4.a .36 .35 .35 .33 .34 .11 .07 .08
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.3 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
2qoh.b
3ms9.a
3mss.c
3pyy.a
4zog.b
1opj.b
2fo0.a
3k5v.a
5mo4.a
[1] 2qoh.b
0
0.7 0.7 0.4 1.9 7.0 6.9 6.8 6.7
[1] 3ms9.a 0.7
0
0.2 0.6 0.5 2.0 1.9 1.5 1.7
[1] 3mss.c 0.7 0.2
0
0.6 0.5 2.1 1.9 1.5 1.8
[1] 3pyy.a 0.4 0.6 0.6
0
0.5 2.7 2.4 2.0 2.2
[1] 4zog.b 1.9 0.5 0.5 0.5
0
3.2 2.9 2.6 2.7
[2] 1opj.b 7.0 2.0 2.1 2.7 3.2
0
0.8 0.9 0.9
[2] 2fo0.a 6.9 1.9 1.9 2.4 2.9 0.8
0
0.7 0.6
[2] 3k5v.a 6.8 1.5 1.5 2.0 2.6 0.9 0.7
0
0.6
[2] 5mo4.a 6.7 1.7 1.8 2.2 2.7 0.9 0.6 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.5 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
2qoh.b
3ms9.a
3mss.c
3pyy.a
4zog.b
1opj.b
2fo0.a
3k5v.a
5mo4.a
[1] 2qoh.b
0
1.2 1.1 1.3 2.3 7.4 7.3 7.2 7.1
[1] 3ms9.a 1.2
0
0.6 0.8 0.8 2.8 2.6 2.3 2.4
[1] 3mss.c 1.1 0.6
0
1.0 0.9 2.9 2.8 2.5 2.5
[1] 3pyy.a 1.3 0.8 1.0
0
1.0 3.3 2.9 2.7 2.7
[1] 4zog.b 2.3 0.8 0.9 1.0
0
3.8 3.5 3.3 3.2
[2] 1opj.b 7.4 2.8 2.9 3.3 3.8
0
0.9 1.1 1.1
[2] 2fo0.a 7.3 2.6 2.8 2.9 3.5 0.9
0
0.9 0.9
[2] 3k5v.a 7.2 2.3 2.5 2.7 3.3 1.1 0.9
0
0.8
[2] 5mo4.a 7.1 2.4 2.5 2.7 3.2 1.1 0.9 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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