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ABL1_HUMAN_228_509_pep

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 (252, 367, 384:388, 390:405, 411:413, 438, 445, 446, 449, 450)252, 367, 384:388, 390:405, 411:413, 438, 445, 446, 449, 450

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, 6bl8 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Q
2
5
2
R
3
6
7
R
3
8
6
L
3
8
7
M
3
8
8
H
3
9
6
A
3
9
7
G
3
9
8
A
3
9
9
K
4
0
0
F
4
0
1
P
4
0
2
I
4
0
3
K
4
0
4
W
4
0
5
L
4
1
1
A
4
1
2
Y
4
1
3
S
4
3
8
L
4
4
5
S
4
4
6
Y
4
4
9
[1]2g1t.a EIFGEFEA66 . . . . . . . . . . . . . . . . . . . . . .
[1]2g1t.b EEIFGEFEAK76 . . . . . . . . . . . . . . . . . . . . . .
[1]2g1t.c EIFGEFE57 . . . . . . . . . . . . . . . . . . . . . .
[1]2g1t.d EEIFGEFE70 . . . . . . . . . . . . . . . . . . . . . .
[1]2g2f.a EAIFAAPF57 . . . . . P . . . . . . . . . . . . . . . .
[1]2g2h.a none . . . . . P . . . . . . . . . . . . . . . .
[1]2g2i.a EEIFGEFE48 - . . . . P . . . . . . . . . . . . . . . .
[1]2g2i.b EEIFGEF49 - . . . . P . . . . . . . . . . . . . . . .
[1]2v7a.a none . . . . . . . . . . . . . . . . . . . . . .
[1]3dk3.a none . . . . . . . . . . . . . . . . . . . P . .
[1]3dk6.a none . . . . . . . . . . . . . . . . . . . P . .
[1]5hu9.a 66k43 . . . . . - - . . . . . . . . . . . . . . .
[2]3oxz.a none . . - - - Y T . . . . . . . . . . . . . . .
[3]3kfa.b none . . . . . . . . . . . . . . . . . . . . . .

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
Q
2
5
2
R
3
6
7
L
3
8
4
S
3
8
5
R
3
8
6
L
3
8
7
M
3
8
8
G
3
9
0
D
3
9
1
T
3
9
2
Y
3
9
3
T
3
9
4
A
3
9
5
H
3
9
6
A
3
9
7
G
3
9
8
A
3
9
9
K
4
0
0
F
4
0
1
P
4
0
2
I
4
0
3
K
4
0
4
W
4
0
5
L
4
1
1
A
4
1
2
Y
4
1
3
S
4
3
8
L
4
4
5
S
4
4
6
Y
4
4
9
E
4
5
0
[1]2g1t.a . . . . . . . . * . . . . . . . * * * . . . . . . . . . . . .
[1]2g1t.b . . . . . . . . . . . . . . . . * * * . . . . . . . . . . . .
[1]2g1t.c . . . . . . . . . . . . . . . . * * * . . . . . . . . . . . .
[1]2g1t.d . . . . . . . . . . . . . . . . * * * . . . . . . . . . . . .
[1]2g2f.a . . . . . . . . . . . . . P . * * . . . . . . . . . . . . . .
[1]2g2h.a . . . . . . . . . . . . . P . * * . . . . . . . . . . . . . .
[1]2g2i.a - . . . . . . . . . . . . P . * * . . . . . . . . . . . . . .
[1]2g2i.b - . . . . . . . . . . . . P . * * * . . . . . . . . . . . . .
[1]2v7a.a . . . . . . . . . . * . . . . * * * . . . . . . . . . . . . .
[1]3dk3.a . . . . . . . . . . F . . . . * * . . . . . . . . . . P . . .
[1]3dk6.a . . . . . . . . . . * . . . . * * . . . . . . . . . . P . . .
[1]5hu9.a . . . . . . . - - - - - - - - * * * * . . . . . . . . . . . .
[2]3oxz.a . . . . - - - - - - - - - Y T * * . . . . . . . . . . . . . .
[3]3kfa.b . . . . . . . . * * * * * * . * * . . . . . . . . . . . . . .

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
2g1t.a:EIFGEFEA
2g1t.b:EEIFGEFEAK
2g1t.c:EIFGEFE
2g1t.d:EEIFGEFE
2g2f.a:EAIFAAPF
2g2h.a is apo
2g2i.a:EEIFGEFE
2g2i.b:EEIFGEF
2v7a.a is apo
3dk3.a is apo
3dk6.a is apo
5hu9.a:66k
3oxz.a is apo
3kfa.b is apo
[1] 2g1t.a
0
0.1 0.2 0.3 4.2 - 1.8 2.2 - - - 5.5 - -
[1] 2g1t.b 0.6
0
0.4 0.2 2.7 - 0.8 1.7 - - - 4.0 - -
[1] 2g1t.c 0.2 0.1
0
0.1 2.6 - 0.6 1.4 - - - 3.9 - -
[1] 2g1t.d 0 0.2 0.1
0
2.9 - 1.0 1.7 - - - 3.7 - -
[1] 2g2f.a 0.1 0 0 0.2
0
- 0 0.1 - - - 4.0 - -
[1] 2g2h.a 0.3 0.1 0.1 0.4 0.3
-
0 0.1 - - - 4.7 - -
[1] 2g2i.a 0.5 0.2 0.1 0.2 0.2 -
0
0.1 - - - 4.3 - -
[1] 2g2i.b 0.1 0 0 0 0.3 - 0
0.1
- - - 4.4 - -
[1] 2v7a.a 0.6 0.2 0.8 1.0 0.3 - 0.2 0.4
-
- - 4.5 - -
[1] 3dk3.a 0.5 0.3 0.3 0.3 0.2 - 0 0.1 -
-
- 4.6 - -
[1] 3dk6.a 0.1 0.1 0.1 0.5 0.4 - 0 0.2 - -
-
4.9 - -
[1] 5hu9.a 8.5 9.0 9.0 9.2 11 - 10 10 - - -
0
- -
[2] 3oxz.a 8.9 9.0 9.2 8.7 10 - 10 9.6 - - - 5.0
-
-
[3] 3kfa.b 20 20 20 20 24 - 22 21 - - - 11 -
-
[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
2g1t.a
2g1t.b
2g1t.c
2g1t.d
2g2f.a
2g2h.a
2g2i.a
2g2i.b
2v7a.a
3dk3.a
3dk6.a
5hu9.a
3oxz.a
3kfa.b
[1] 2g1t.a
0
.12 .12 .08 .17 .21 .17 .14 .21 .18 .19 .25 .49 .93
[1] 2g1t.b .12
0
.04 .06 .15 .18 .15 .13 .17 .17 .18 .24 .44 .95
[1] 2g1t.c .12 .04
0
.06 .16 .18 .16 .13 .14 .17 .18 .22 .46 .99
[1] 2g1t.d .08 .06 .06
0
.13 .15 .13 .10 .16 .14 .16 .24 .44 .96
[1] 2g2f.a .17 .15 .16 .13
0
.06 .02 .04 .09 .06 .06 .25 .37 .91
[1] 2g2h.a .21 .18 .18 .15 .06
0
.07 .07 .12 .05 .04 .23 .37 .90
[1] 2g2i.a .17 .15 .16 .13 .02 .07
0
.04 .10 .06 .07 .24 .38 .91
[1] 2g2i.b .14 .13 .13 .10 .04 .07 .04
0
.09 .06 .06 .21 .36 .91
[1] 2v7a.a .21 .17 .14 .16 .09 .12 .10 .09
0
.11 .12 .22 .44 .99
[1] 3dk3.a .18 .17 .17 .14 .06 .05 .06 .06 .11
0
.03 .23 .37 .92
[1] 3dk6.a .19 .18 .18 .16 .06 .04 .07 .06 .12 .03
0
.23 .37 .93
[1] 5hu9.a .25 .24 .22 .24 .25 .23 .24 .21 .22 .23 .23
0
.51 1.0
[2] 3oxz.a .49 .44 .46 .44 .37 .37 .38 .36 .44 .37 .37 .51
0
.78
[3] 3kfa.b .93 .95 .99 .96 .91 .90 .91 .91 .99 .92 .93 1.0 .78
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 6.9 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
2g1t.a
2g1t.b
2g1t.c
2g1t.d
2g2f.a
2g2h.a
2g2i.a
2g2i.b
2v7a.a
3dk3.a
3dk6.a
5hu9.a
3oxz.a
3kfa.b
[1] 2g1t.a
0
1.0 1.2 1.6 11 11 10 10 10 11 11 6.9 5.5 9.2
[1] 2g1t.b 1.0
0
0.6 1.2 10 11 10 10 10 11 11 7.0 5.5 9.6
[1] 2g1t.c 1.2 0.6
0
0.9 10 10 9.9 9.9 10 11 11 7.0 5.6 9.7
[1] 2g1t.d 1.6 1.2 0.9
0
10 10 9.8 9.7 10 10 10 7.0 5.9 10
[1] 2g2f.a 11 10 10 10
0
1.4 2.3 2.4 2.3 1.3 1.4 8.8 6.6 15
[1] 2g2h.a 11 11 10 10 1.4
0
2.4 2.5 2.5 0.7 0.6 8.4 6.2 14
[1] 2g2i.a 10 10 9.9 9.8 2.3 2.4
0
0.7 0.8 2.4 2.4 8.0 5.8 14
[1] 2g2i.b 10 10 9.9 9.7 2.4 2.5 0.7
0
0.8 2.6 2.6 8.0 5.9 14
[1] 2v7a.a 10 10 10 10 2.3 2.5 0.8 0.8
0
2.5 2.5 8.2 6.2 15
[1] 3dk3.a 11 11 11 10 1.3 0.7 2.4 2.6 2.5
0
0.3 8.8 6.5 15
[1] 3dk6.a 11 11 11 10 1.4 0.6 2.4 2.6 2.5 0.3
0
8.8 6.4 15
[1] 5hu9.a 6.9 7.0 7.0 7.0 8.8 8.4 8.0 8.0 8.2 8.8 8.8
0
4.5 6.1
[2] 3oxz.a 5.5 5.5 5.6 5.9 6.6 6.2 5.8 5.9 6.2 6.5 6.4 4.5
0
2.8
[3] 3kfa.b 9.2 9.6 9.7 10 15 14 14 14 15 15 15 6.1 2.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 6.9 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
2g1t.a
2g1t.b
2g1t.c
2g1t.d
2g2f.a
2g2h.a
2g2i.a
2g2i.b
2v7a.a
3dk3.a
3dk6.a
5hu9.a
3oxz.a
3kfa.b
[1] 2g1t.a
0
1.3 1.4 1.8 10 10 9.7 9.7 10 11 11 6.9 5.3 9.4
[1] 2g1t.b 1.3
0
0.8 1.5 9.8 10 9.4 9.4 9.9 10 10 6.9 5.3 9.6
[1] 2g1t.c 1.4 0.8
0
1.3 9.8 10 9.3 9.3 9.7 10 10 7.0 5.4 9.7
[1] 2g1t.d 1.8 1.5 1.3
0
9.7 10 9.2 9.2 9.6 10 10 7.0 5.7 10
[1] 2g2f.a 10 9.8 9.8 9.7
0
2.0 3.2 3.3 3.4 1.9 1.3 8.8 6.0 14
[1] 2g2h.a 10 10 10 10 2.0
0
3.4 3.4 3.8 1.1 1.0 8.4 5.5 14
[1] 2g2i.a 9.7 9.4 9.3 9.2 3.2 3.4
0
1.0 1.3 3.4 3.4 7.8 5.1 14
[1] 2g2i.b 9.7 9.4 9.3 9.2 3.3 3.4 1.0
0
1.5 3.5 3.5 7.8 5.2 14
[1] 2v7a.a 10 9.9 9.7 9.6 3.4 3.8 1.3 1.5
0
3.8 3.7 8.2 6.0 14
[1] 3dk3.a 11 10 10 10 1.9 1.1 3.4 3.5 3.8
0
0.5 8.8 5.8 14
[1] 3dk6.a 11 10 10 10 1.3 1.0 3.4 3.5 3.7 0.5
0
8.9 5.9 14
[1] 5hu9.a 6.9 6.9 7.0 7.0 8.8 8.4 7.8 7.8 8.2 8.8 8.9
0
3.8 5.8
[2] 3oxz.a 5.3 5.3 5.4 5.7 6.0 5.5 5.1 5.2 6.0 5.8 5.9 3.8
0
3.0
[3] 3kfa.b 9.4 9.6 9.7 10 14 14 14 14 14 14 14 5.8 3.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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