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ABL1_HUMAN_61_120_SH3

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: SH3 (70, 72, 75:79, 94, 98, 99, 110, 112, 114, 115)
219:235
70, 72, 75:79, 94, 98, 99, 110, 112, 114, 115, 219:235, 264, 296, 300:302, 378

Full PDB list

1abo, 1abq, 1bbz, 1opk, 1opl, 2abl, 2fo0, 2o88, 3eg0, 3eg1, 3eg2, 3eg3, 3egu, 4j9b, 4j9c, 4j9d, 4j9e, 4j9f, 4j9g, 4j9h, 4j9i, 4jjb, 4jjc, 4jjd, 5mo4, 5oaz (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
7
0
F
7
2
S
7
5
D
7
7
N
7
8
T
7
9
N
9
4
E
9
8
W
9
9
W
1
1
0
P
1
1
2
N
1
1
4
Y
1
1
5
[1]1abo.a APTMPPPLPP71 . . . . . . . . . . . . .
[1]1bbz.a aceAPSYSPPPPP75 . . . . . . . . . . . . .
[1]2o88.a aceAPSYSPPPPP75 . . . . . . . . . . . A .
[1]3eg0.a none . . . . . . . . . . . T .
[1]3eg1.a aceAPSYSPPPPP75 . . . . . . . . . . . Q .
[1]3eg2.a none . . . . . . . . . . . Q .
[1]3egu.a none . . . . . . . . . . . A .
[1]4j9c.a aceAPTYSPPLPP77 . . . . . . . . . . . . .
[1]4j9d.c aceAPTYPPPLPP78 . . . . . . . . . . . A .
[1]4j9e.c aceAPTYSPPLPP77 . . . . . . . . . . . A .
[1]4j9f.c aceAPTYPPPLPP78 . . . . . . . . . . . . .
[1]4j9h.b aceAPTYPPPPPP77 . . . . . . . . . . . . .
[2]1opk.a none . . . . . . . . . . . . .
[2]5mo4.a 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
Y
7
0
F
7
2
S
7
5
G
7
6
D
7
7
N
7
8
T
7
9
N
9
4
E
9
8
W
9
9
W
1
1
0
P
1
1
2
N
1
1
4
Y
1
1
5
K
2
1
9
R
2
2
0
N
2
2
1
K
2
2
2
P
2
2
3
T
2
2
4
V
2
2
5
Y
2
2
6
G
2
2
7
V
2
2
8
S
2
2
9
P
2
3
0
N
2
3
1
Y
2
3
2
D
2
3
3
K
2
3
4
W
2
3
5
Y
2
6
4
P
2
9
6
Q
3
0
0
L
3
0
1
L
3
0
2
K
3
7
8
[1]1abo.a . . . . . . . . . . . . . . - - - - - - - - - - - - - - - - - - - - - - -
[1]1bbz.a . . . . . . . . . . . . . . - - - - - - - - - - - - - - - - - - - - - - -
[1]2o88.a . . . . . . . . . . . . A . - - - - - - - - - - - - - - - - - - - - - - -
[1]3eg0.a . . . . . . . . . . . . T . - - - - - - - - - - - - - - - - - - - - - - -
[1]3eg1.a . . . . . . . . . . . . Q . - - - - - - - - - - - - - - - - - - - - - - -
[1]3eg2.a . . . . . . . . . . . . Q . - - - - - - - - - - - - - - - - - - - - - - -
[1]3egu.a . . . . . . . . . . . . A . - - - - - - - - - - - - - - - - - - - - - - -
[1]4j9c.a . . . . . . . . . . . . . . - - - - - - - - - - - - - - - - - - - - - - -
[1]4j9d.c . . . . . . . . . . . . A . - - - - - - - - - - - - - - - - - - - - - - -
[1]4j9e.c . . . . . . . . . . . . A . - - - - - - - - - - - - - - - - - - - - - - -
[1]4j9f.c . . . . . . . . . . . . . . - - - - - - - - - - - - - - - - - - - - - - -
[1]4j9h.b . . . . . . . . . . . . . . - - - - - - - - - - - - - - - - - - - - - - -
[2]1opk.a . . . . . * . . . . . . . . . . * * * * I * * * * * * . . * . . . . . . .
[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
1abo.a:APTMPPPLPP
1bbz.a:aceAPSYSPPPPP
2o88.a:aceAPSYSPPPPP
3eg0.a is apo
3eg1.a:aceAPSYSPPPPP
3eg2.a is apo
3egu.a is apo
4j9c.a:aceAPTYSPPLPP
4j9d.c:aceAPTYPPPLPP
4j9e.c:aceAPTYSPPLPP
4j9f.c:aceAPTYPPPLPP
4j9h.b:aceAPTYPPPPPP
1opk.a is apo
5mo4.a is apo
[1] 1abo.a
0
0.4 0.3 - 0.3 - - 0.5 0.4 0.2 0.1 0.2 - -
[1] 1bbz.a 0.1
0
0.1 - 0 - - 0.2 0 0 0 0 - -
[1] 2o88.a 0.1 0
0
- 0 - - 0.1 0.2 0 0 0.1 - -
[1] 3eg0.a 0.1 0 0
-
0 - - 0.2 0.1 0 0.1 0.1 - -
[1] 3eg1.a 0.2 0.1 0.2 -
0
- - 0.1 0 0 0 0 - -
[1] 3eg2.a 1.2 1.2 0.9 - 1.4
-
- 1.9 1.8 1.4 1.5 1.9 - -
[1] 3egu.a 0.1 0.3 0.1 - 0.3 -
-
0.4 0.3 0.2 0.3 0.5 - -
[1] 4j9c.a 0.3 0.1 0 - 0 - -
0
0 0 0 0.1 - -
[1] 4j9d.c 0.3 0 0.1 - 0 - - 0.1
0
0 0 0 - -
[1] 4j9e.c 0.1 0 0 - 0 - - 0 0
0
0 0 - -
[1] 4j9f.c 0.2 0 0 - 0.1 - - 0.1 0 0
0
0 - -
[1] 4j9h.b 0.2 0 0 - 0.1 - - 0 0 0 0
0
- -
[2] 1opk.a 34 32 31 - 33 - - 34 36 36 36 36
-
-
[2] 5mo4.a 32 29 28 - 31 - - 31 33 32 33 33 -
-
[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
1abo.a
1bbz.a
2o88.a
3eg0.a
3eg1.a
3eg2.a
3egu.a
4j9c.a
4j9d.c
4j9e.c
4j9f.c
4j9h.b
1opk.a
5mo4.a
[1] 1abo.a
0
.02 .02 .02 .02 .06 .03 .02 .02 .02 .02 .02 1.1 .98
[1] 1bbz.a .02
0
.01 .01 .01 .05 .02 .01 .01 .01 .01 .01 1.0 .97
[1] 2o88.a .02 .01
0
.01 .01 .05 .02 .01 .01 .01 .01 .01 1.0 .97
[1] 3eg0.a .02 .01 .01
0
.01 .05 .01 .01 .01 .01 .01 .01 1.0 .96
[1] 3eg1.a .02 .01 .01 .01
0
.06 .03 .01 .01 .01 .01 .01 1.0 .97
[1] 3eg2.a .06 .05 .05 .05 .06
0
.05 .06 .06 .05 .06 .06 1.1 .97
[1] 3egu.a .03 .02 .02 .01 .03 .05
0
.03 .03 .02 .02 .02 1.0 .96
[1] 4j9c.a .02 .01 .01 .01 .01 .06 .03
0
.01 .01 .01 .01 1.0 .97
[1] 4j9d.c .02 .01 .01 .01 .01 .06 .03 .01
0
.01 .01 .01 1.1 .98
[1] 4j9e.c .02 .01 .01 .01 .01 .05 .02 .01 .01
0
.01 0 1.0 .97
[1] 4j9f.c .02 .01 .01 .01 .01 .06 .02 .01 .01 .01
0
0 1.0 .97
[1] 4j9h.b .02 .01 .01 .01 .01 .06 .02 .01 .01 0 0
0
1.0 .97
[2] 1opk.a 1.1 1.0 1.0 1.0 1.0 1.1 1.0 1.0 1.1 1.0 1.0 1.0
0
.12
[2] 5mo4.a .98 .97 .97 .96 .97 .97 .96 .97 .98 .97 .97 .97 .12
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
1abo.a
1bbz.a
2o88.a
3eg0.a
3eg1.a
3eg2.a
3egu.a
4j9c.a
4j9d.c
4j9e.c
4j9f.c
4j9h.b
1opk.a
5mo4.a
[1] 1abo.a
0
0.4 0.4 0.5 0.4 1.0 0.6 0.4 0.4 0.5 0.4 0.5 1.1 1.2
[1] 1bbz.a 0.4
0
0.2 0.4 0.3 0.9 0.7 0.3 0.4 0.5 0.4 0.3 1.1 1.1
[1] 2o88.a 0.4 0.2
0
0.5 0.3 0.9 0.7 0.3 0.5 0.5 0.5 0.4 1.0 1.0
[1] 3eg0.a 0.5 0.4 0.5
0
0.4 0.9 0.7 0.3 0.5 0.5 0.5 0.4 1.1 1.1
[1] 3eg1.a 0.4 0.3 0.3 0.4
0
0.9 0.7 0.3 0.4 0.5 0.4 0.3 1.1 1.1
[1] 3eg2.a 1.0 0.9 0.9 0.9 0.9
0
1.2 0.9 1.0 1.1 1.0 0.9 1.1 1.0
[1] 3egu.a 0.6 0.7 0.7 0.7 0.7 1.2
0
0.7 0.6 0.6 0.7 0.7 1.1 1.1
[1] 4j9c.a 0.4 0.3 0.3 0.3 0.3 0.9 0.7
0
0.3 0.4 0.3 0.2 1.0 1.0
[1] 4j9d.c 0.4 0.4 0.5 0.5 0.4 1.0 0.6 0.3
0
0.2 0.2 0.3 1.1 1.2
[1] 4j9e.c 0.5 0.5 0.5 0.5 0.5 1.1 0.6 0.4 0.2
0
0.2 0.4 1.1 1.1
[1] 4j9f.c 0.4 0.4 0.5 0.5 0.4 1.0 0.7 0.3 0.2 0.2
0
0.2 1.1 1.1
[1] 4j9h.b 0.5 0.3 0.4 0.4 0.3 0.9 0.7 0.2 0.3 0.4 0.2
0
1.1 1.1
[2] 1opk.a 1.1 1.1 1.0 1.1 1.1 1.1 1.1 1.0 1.1 1.1 1.1 1.1
0
0.8
[2] 5mo4.a 1.2 1.1 1.0 1.1 1.1 1.0 1.1 1.0 1.2 1.1 1.1 1.1 0.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
1abo.a
1bbz.a
2o88.a
3eg0.a
3eg1.a
3eg2.a
3egu.a
4j9c.a
4j9d.c
4j9e.c
4j9f.c
4j9h.b
1opk.a
5mo4.a
[1] 1abo.a
0
0.7 0.8 0.9 0.7 1.5 1.0 0.7 0.8 1.1 0.9 0.8 1.9 1.4
[1] 1bbz.a 0.7
0
0.6 0.8 0.4 1.4 0.9 0.4 0.6 1.0 0.7 0.5 1.7 1.2
[1] 2o88.a 0.8 0.6
0
0.7 0.5 1.4 0.9 0.6 0.8 1.0 0.9 0.7 1.7 1.2
[1] 3eg0.a 0.9 0.8 0.7
0
0.8 1.5 0.9 0.8 0.9 0.8 0.9 0.7 1.8 1.2
[1] 3eg1.a 0.7 0.4 0.5 0.8
0
1.4 0.9 0.4 0.7 0.9 0.7 0.5 1.8 1.3
[1] 3eg2.a 1.5 1.4 1.4 1.5 1.4
0
1.5 1.4 1.4 1.5 1.6 1.4 1.8 1.4
[1] 3egu.a 1.0 0.9 0.9 0.9 0.9 1.5
0
0.8 0.9 0.8 0.9 0.8 1.6 1.1
[1] 4j9c.a 0.7 0.4 0.6 0.8 0.4 1.4 0.8
0
0.6 0.9 0.6 0.4 1.7 1.3
[1] 4j9d.c 0.8 0.6 0.8 0.9 0.7 1.4 0.9 0.6
0
0.7 0.7 0.6 1.9 1.4
[1] 4j9e.c 1.1 1.0 1.0 0.8 0.9 1.5 0.8 0.9 0.7
0
0.9 0.8 1.7 1.3
[1] 4j9f.c 0.9 0.7 0.9 0.9 0.7 1.6 0.9 0.6 0.7 0.9
0
0.5 1.9 1.4
[1] 4j9h.b 0.8 0.5 0.7 0.7 0.5 1.4 0.8 0.4 0.6 0.8 0.5
0
1.7 1.2
[2] 1opk.a 1.9 1.7 1.7 1.8 1.8 1.8 1.6 1.7 1.9 1.7 1.9 1.7
0
1.1
[2] 5mo4.a 1.4 1.2 1.2 1.2 1.3 1.4 1.1 1.3 1.4 1.3 1.4 1.2 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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