KLIFS - the structural kinase database

Structure information


PDB:	3OXZ
PubMed:	21118377
Release date:	2010-12-15
Resolution:	2.2 Å

Kinase:	Abl1 (ABL1)
Family:	Abl
Group:	TK
Species:	MOUSE

Quality Score:	8.8
Missing Residues:	0
Missing Atoms:	12

DFG conformation:	out
αC-helix conformation:	in
Salt bridge K^III.17 and E^αC.24:	Yes (3Å)


ASP rotation (xDFG.81) :	199°
PHE rotation (xDFG.82) :	199°
Activation loop position:	2.2Å
αC-helix position:	18.3Å

G-rich loop angle:	57.4°
G-rich loop distance:	17.4Å
G-rich loop rotation:	11.8°

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

I1

H-bond protein

Binding pocket sequence

Uniprot	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS
Structure:	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS

Modified residues

No modified residues identified.

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

Download image
LABELS
KLIFS residue #
Amino Acid
None
COLORS
Interaction types
KLIFS (all res.)
KLIFS (interacting res.)
None
OTHER
Show/hide non-interacting res.
En/disable resizing interacting res.

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

■ 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 T
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

■▲

■♦

Interaction pattern search

Search KLIFS for kinase-ligand complexes with similar interaction patterns:

Binding affinities

ChEMBL ID:CHEMBL1171837
Bioaffinities: 119 records for 62 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Breakpoint cluster region protein	7.3	7.3	7.3	pKd	2
Homo sapiens	CaM-kinase kinase beta	5.8	5.8	5.8	pKd	1
Homo sapiens	c-Jun N-terminal kinase 2	5.1	5.1	5.1	pKd	1
Homo sapiens	Discoidin domain-containing receptor 2	7.1	7.1	7.1	pKd	1
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 5	5.5	5.5	5.5	pKd	1
Homo sapiens	Ephrin type-A receptor 1	5.9	5.9	5.9	pKd	1
Homo sapiens	Ephrin type-A receptor 2	7.6	7.6	7.6	pKd	1
Homo sapiens	Ephrin type-A receptor 4	4.8	4.8	4.8	pKd	1
Homo sapiens	Ephrin type-A receptor 5	8.1	8.1	8.1	pKd	1
Homo sapiens	Ephrin type-B receptor 2	5.7	5.7	5.7	pKd	1
Homo sapiens	Ephrin type-B receptor 3	6.3	6.3	6.3	pKd	1
Homo sapiens	Ephrin type-B receptor 4	5.8	5.8	5.8	pKd	1
Homo sapiens	Epithelial discoidin domain-containing receptor 1	7.8	7.8	7.8	pKd	1
Homo sapiens	Fibroblast growth factor receptor 1	8.9	8.7	9.2	pIC50	6
Homo sapiens	Fibroblast growth factor receptor 2	8.7	8.7	8.9	pIC50	2
Homo sapiens	Fibroblast growth factor receptor 3	7.8	7.8	8	pIC50	2
Homo sapiens	Fibroblast growth factor receptor 4	8.1	8.1	8.2	pIC50	2
Homo sapiens	Interleukin-1 receptor-associated kinase 1	6.2	6.2	6.2	pKd	1
Homo sapiens	Interleukin-1 receptor-associated kinase 4	5.7	5.7	5.7	pKd	1
Homo sapiens	MAP kinase-activated protein kinase 2	6.3	6.3	6.3	pKd	1
Homo sapiens	MAP kinase p38 alpha	6.8	6.8	6.8	pKd	1
Homo sapiens	MAP kinase p38 beta	6	6	6	pKd	1
Homo sapiens	Maternal embryonic leucine zipper kinase	5.5	5.5	5.5	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 1	6.3	6.3	6.3	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 1	6.1	6.1	6.1	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 2	7.4	7.4	7.4	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 4	6.5	6.5	6.5	pKd	1
Homo sapiens	Mixed lineage kinase 7	7.4	7.4	7.4	pKd	1
Homo sapiens	Myosin light chain kinase, smooth muscle	7	7	7	pKd	1
Homo sapiens	Non-receptor tyrosine-protein kinase TNK1	7.1	7.1	7.1	pKd	1
Homo sapiens	Platelet-derived growth factor receptor alpha	8.6	8.6	8.6	pIC50	1
Homo sapiens	Platelet-derived growth factor receptor beta	8.9	8.9	8.9	pIC50	1
Homo sapiens	Platelet-derived growth factor receptor beta	5.5	5.5	5.5	pKd	1
Homo sapiens	Protein tyrosine kinase 2 beta	6.5	6.5	6.5	pKd	1
Homo sapiens	Receptor-interacting serine/threonine-protein kinase 1	7.9	7.9	7.9	pIC50	1
Homo sapiens	Receptor-interacting serine/threonine-protein kinase 3	8.8	8.8	8.8	pIC50	1
Homo sapiens	Receptor-interacting serine/threonine-protein kinase 3	7.6	7.6	7.6	pKd	1
Homo sapiens	Serine/threonine-protein kinase B-raf	5.9	5.9	5.9	pKd	1
Homo sapiens	Serine/threonine-protein kinase GAK	5.7	5.7	5.7	pKd	1
Homo sapiens	Serine/threonine-protein kinase PCTAIRE-1	5.8	5.8	5.8	pKd	1
Homo sapiens	Serine/threonine-protein kinase PCTAIRE-2	6.5	6.5	6.5	pKd	1
Homo sapiens	Serine/threonine-protein kinase RIPK2	8.2	8.2	9	pIC50	2
Homo sapiens	Serine/threonine-protein kinase RIPK2	7.1	7.1	7.1	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO3	5.7	5.7	5.7	pKd	1
Homo sapiens	Serine/threonine-protein kinase ULK3	5.8	5.8	5.8	pKd	1
Homo sapiens	Stem cell growth factor receptor	7.8	6.9	8.8	pIC50	6
Homo sapiens	TGF-beta receptor type II	5.8	5.8	5.8	pKd	1
Homo sapiens	TRAF2- and NCK-interacting kinase	6.4	6.4	6.4	pKd	1
Homo sapiens	Tyrosine-protein kinase ABL	9	7.4	9.5	pIC50	23
Homo sapiens	Tyrosine-protein kinase ABL	7.4	7.4	7.4	pKd	1
Homo sapiens	Tyrosine-protein kinase ABL2	7.7	7.7	7.7	pKd	1
Homo sapiens	Tyrosine-protein kinase BTK	5.7	5.7	5.7	pKd	1
Homo sapiens	Tyrosine-protein kinase CSK	6.5	6.5	6.5	pKd	1
Homo sapiens	Tyrosine-protein kinase FGR	7.4	7.4	7.4	pKd	1
Homo sapiens	Tyrosine-protein kinase FRK	7	7	7	pKd	1
Homo sapiens	Tyrosine-protein kinase FYN	7.4	7.4	7.4	pKd	1
Homo sapiens	Tyrosine-protein kinase HCK	7.1	7.1	7.1	pKd	1
Homo sapiens	Tyrosine-protein kinase LCK	7.6	7.6	7.6	pKd	1
Homo sapiens	Tyrosine-protein kinase Lyn	8.7	8.7	9.6	pIC50	2
Homo sapiens	Tyrosine-protein kinase Lyn	7.6	7.6	7.6	pKd	1
Homo sapiens	Tyrosine-protein kinase receptor FLT3	9.5	9.5	9.5	pIC50	1
Homo sapiens	Tyrosine-protein kinase receptor FLT3	8.2	8.2	8.2	pKd	1
Homo sapiens	Tyrosine-protein kinase receptor RET	7.6	7.5	9.5	pIC50	4
Homo sapiens	Tyrosine-protein kinase receptor RET	7.6	7.6	7.6	pKd	1
Gallus gallus	Tyrosine-protein kinase SRC	9.1	9.1	9.1	pIC50	1
Homo sapiens	Tyrosine-protein kinase SRC	8.5	8	8.6	pIC50	3
Homo sapiens	Tyrosine-protein kinase SRC	6.4	6.4	6.4	pKd	1
Homo sapiens	Tyrosine-protein kinase YES	6.7	6.7	6.7	pKd	1
Homo sapiens	Vascular endothelial growth factor receptor 1	7.7	7.7	7.7	pIC50	1
Homo sapiens	Vascular endothelial growth factor receptor 2	8.7	7.6	8.8	pIC50	7

3OXZ - chain A | C-abl oncogene 1, non-receptor tyrosine kinase