3IK3 - chain B | C-abl oncogene 1, non-receptor tyrosine kinase
Structure information
PDB:3IK3
PubMed:19878872
Release date:2009-11-03
Resolution:1.9 Å
 
Kinase:Abl1 (ABL1)
Family:Abl
Group:TK
Species:MOUSE
 
Quality Score:8
Missing Residues:0
Missing Atoms:0
DFG conformation:out
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes
 
 
ASP rotation (xDFG.81) :198°
PHE rotation (xDFG.82) :195°
Activation loop position:2.1Å
αC-helix position:18.6Å
 
G-rich loop angle:57.8°
G-rich loop distance:17.7Å
G-rich loop rotation:10.6°
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I4
H-bond protein
Binding pocket sequence
UniprotHKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS
Structure:HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIIIEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: 0LI
Ligand Name: 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzamide

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  • LABELS
  • KLIFS residue #
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  • COLORS
  • Interaction types
  • KLIFS (all res.)
  • KLIFS (interacting res.)
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This ligand targets the following (sub)pockets:
Main pockets
Front

Gate

Back

Subpockets
FP-I

FP-II

BP-I-A

BP-I-B

BP-II-in

BP-II-A-in

BP-II-B-in

BP-II-out

BP-II-B

BP-III

BP-IV

BP-V

Kinase-ligand interactions
Kinase-ligand interaction pattern
Hydrophobic Aromatic face-to-face Aromatic face-to-edge H-bond donor H-bond acceptor Ionic positive Ionic negative
I g.l II III αC
1 H
246
2 K
247
3 L
248
4 G
249
5 G
250
6 G
251
7 Q
252
8 Y
253
9 G
254
10 E
255
11 V
256
12 Y
257
13 E
258
14 V
268
15 A
269
16 V
270
17 K
271
18 T
272
19 L
273
20 E
282
αC b.l IV
21 F
283
22 L
284
23 K
285
24 E
286
25 A
287
26 A
288
27 V
289
28 M
290
29 K
291
30 E
292
31 I
293
32 K
294
33 P
296
34 N
297
35 L
298
36 V
299
37 Q
300
38 L
301
39 L
302
40 G
303
IV V GK hinge linker αD αE
41 V
304
42 Y
312
43 I
313
44 I
314
45 I
315
46 E
316
47 F
317
48 M
318
49 T
319
50 Y
320
51 G
321
52 N
322
53 L
323
54 L
324
55 D
325
56 Y
326
57 L
327
58 R
328
59 E
329
60 Y
353
αE VI c.l VII VIII x
61 L
354
62 E
355
63 K
356
64 K
357
65 N
358
66 F
359
67 I
360
68 H
361
69 R
362
70 D
363
71 L
364
72 A
365
73 A
366
74 R
367
75 N
368
76 C
369
77 L
370
78 V
371
79 V
379
80 A
380
DFG a.l
81 D
381
82 F
382
83 G
383
84 L
384
85 S
385

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Binding affinities
ChEMBL ID:CHEMBL1171837
Bioaffinities: 59 records for 18 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensFibroblast growth factor receptor 18.98.79.2pIC506
Homo sapiensFibroblast growth factor receptor 28.78.78.9pIC502
Homo sapiensFibroblast growth factor receptor 37.87.88pIC502
Homo sapiensFibroblast growth factor receptor 48.18.18.2pIC502
Homo sapiensPlatelet-derived growth factor receptor alpha8.68.68.6pIC501
Homo sapiensPlatelet-derived growth factor receptor beta8.98.98.9pIC501
Homo sapiensReceptor-interacting serine/threonine-protein kinase 17.97.97.9pIC501
Homo sapiensReceptor-interacting serine/threonine-protein kinase 38.88.88.8pIC501
Homo sapiensSerine/threonine-protein kinase RIPK28.28.29pIC502
Homo sapiensStem cell growth factor receptor7.86.98.8pIC506
Homo sapiensTyrosine-protein kinase ABL98.19.5pIC5019
Homo sapiensTyrosine-protein kinase Lyn9.69.69.6pIC501
Homo sapiensTyrosine-protein kinase receptor FLT39.59.59.5pIC501
Homo sapiensTyrosine-protein kinase receptor RET7.67.59.5pIC504
Gallus gallusTyrosine-protein kinase SRC9.19.19.1pIC501
Homo sapiensTyrosine-protein kinase SRC8.58.58.6pIC502
Homo sapiensVascular endothelial growth factor receptor 17.77.77.7pIC501
Homo sapiensVascular endothelial growth factor receptor 28.78.48.8pIC506