1OPK - chain A | C-abl oncogene 1, non-receptor tyrosine kinase
Structure information
PDB:1OPK
PubMed:12654251
Release date:2003-04-08
Resolution:1.8 Å
 
Kinase:Abl1 (ABL1)
Family:Abl
Group:TK
Species:MOUSE
 
Quality Score:8
Missing Residues:0
Missing Atoms:0
DFG conformation:out-like
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (2.9Å)
 
 
ASP rotation (xDFG.81) :112°
PHE rotation (xDFG.82) :157°
Activation loop position:-1.3Å
αC-helix position:18.8Å
 
G-rich loop angle:54.8°
G-rich loop distance:16.7Å
G-rich loop rotation:0.5°
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
Binding pocket sequence
UniprotHKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS
Structure:HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRNLAARNCLVVADFGLS


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: P16
Ligand Name: 6-(2,6-DICHLOROPHENYL)-2-{[3-(HYDROXYMETHYL)PHENYL]AMINO}-8-METHYLPYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE

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  • LABELS
  • KLIFS residue #
  • Amino Acid
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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
265
2 K
266
3 L
267
4 G
268
5 G
269
6 G
270
7 Q
271
8 Y
272
9 G
273
10 E
274
11 V
275
12 Y
276
13 E
277
14 V
287
15 A
288
16 V
289
17 K
290
18 T
291
19 L
292
20 E
301
αC b.l IV
21 F
302
22 L
303
23 K
304
24 E
305
25 A
306
26 A
307
27 V
308
28 M
309
29 K
310
30 E
311
31 I
312
32 K
313
33 P
315
34 N
316
35 L
317
36 V
318
37 Q
319
38 L
320
39 L
321
40 G
322
IV V GK hinge linker αD αE
41 V
323
42 Y
331
43 I
332
44 I
333
45 T
334
46 E
335
47 F
336
48 M
337
49 T
338
50 Y
339
51 G
340
52 N
341
53 L
342
54 L
343
55 D
344
56 Y
345
57 L
346
58 R
347
59 E
348
60 Y
372
αE VI c.l VII VIII x
61 L
373
62 E
374
63 K
375
64 K
376
65 N
377
66 F
378
67 I
379
68 H
380
69 R
381
70 N
382
71 L
383
72 A
384
73 A
385
74 R
386
75 N
387
76 C
388
77 L
389
78 V
390
79 V
398
80 A
399
DFG a.l
81 D
400
82 F
401
83 G
402
84 L
403
85 S
404

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Binding affinities
ChEMBL ID:CHEMBL327127
Bioaffinities: 11 records for 8 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensEpidermal growth factor receptor erbB17.17.17.1pIC502
Homo sapiensFibroblast growth factor receptor 17.17.17.2pIC502
Homo sapiensMAP kinase p38 alpha6.96.96.9pIC501
Mus musculusPlatelet-derived growth factor receptor beta6.76.76.7pIC501
Homo sapiensStem cell growth factor receptor6.26.26.2pIC501
Homo sapiensTyrosine-protein kinase ABL8.68.68.6pIC501
Gallus gallusTyrosine-protein kinase SRC8.28.28.2pIC501
Homo sapiensTyrosine-protein kinase SRC7.47.48.3pIC502