KLIFS - the kinase structures database

Version: 3.2
Updated: 29-Oct-2025

ABL proto-oncogene 1, non-receptor tyrosine kinase

Kinase structure
Kinase:	ABL1
Family:	Abl
Group:	TK
Species:	HUMAN
IUPHAR/BPS ID:	1923
PDB:	3CS9
sc-PDB:
KIDFamMap:	Search
Release date:	2008-04-22
PubMed:	15710326
Chain:	A
(Alternate) Model:	A
Orthosteric ligand:	NIL

More entries for 3CS9
3CS9	Alternative model:	A	Chain:	B
3CS9	Alternative model:	A	Chain:	C
3CS9	Alternative model:	A	Chain:	D
3CS9	Alternative model:	B	Chain:	A
3CS9	Alternative model:	B	Chain:	B
3CS9	Alternative model:	B	Chain:	C
3CS9	Alternative model:	B	Chain:	D

Structural information
DFG conformation:	out
αC-helix conformation:	in
G-rich loop angle (distance):	63.4° (18.7Å)
G-rich loop rotation:	15.3°
Quality Score:	7.6
Resolution:	2.21 Å
Missing Residues:	0
Missing Atoms:	0

Ligand binding mode
Pockets	Subpockets	Waters
front gate back	BP-I-A BP-I-B BP-II-out BP-III BP-V	Cluster I1 I4 O1	Ligand No No Yes	Protein Yes Yes No

Pocket alignment
Uniprot sequence:	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS
Sequence structure:	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS

Ligand affinity
ChEMBL ID:	CHEMBL255863
Bioaffinities:	113 records for 53 kinases

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Plasmodium falciparum (isolate 3D7)	Calcium-dependent protein kinase 1	6.1	6.1	6.1	pKd	1
Homo sapiens	c-Jun N-terminal kinase 1	6.4	6.4	6.4	pKd	1
Homo sapiens	c-Jun N-terminal kinase 2	5.2	5.2	5.2	pKd	1
Homo sapiens	c-Jun N-terminal kinase 3	5.7	5.7	5.7	pKd	1
Homo sapiens	Discoidin domain-containing receptor 2	7.8	7	8.7	pIC50	5
Homo sapiens	Discoidin domain-containing receptor 2	7.5	7.1	8.2	pKd	4
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 5	6.7	6.7	6.7	pKd	1
Homo sapiens	Dual specificity protein kinase CLK4	5.2	5.2	5.2	pKd	1
Homo sapiens	Dual specificty protein kinase CLK1	5.7	5.7	5.7	pKd	2
Homo sapiens	Ephrin type-A receptor 1	6.2	6.2	6.2	pKd	1
Homo sapiens	Ephrin type-A receptor 2	6.6	6.6	6.6	pKd	1
Homo sapiens	Ephrin type-A receptor 3	7	7	7	pKd	1
Homo sapiens	Ephrin type-A receptor 4	6.5	6.5	6.5	pKd	1
Homo sapiens	Ephrin type-A receptor 5	5.7	5.7	5.7	pKd	1
Homo sapiens	Ephrin type-A receptor 6	6.2	6.2	6.2	pKd	1
Homo sapiens	Ephrin type-A receptor 8	7.4	7.4	7.4	pKd	1
Homo sapiens	Ephrin type-B receptor 1	5.9	5.9	5.9	pKd	1
Homo sapiens	Ephrin type-B receptor 2	6.2	6.2	6.2	pKd	1
Homo sapiens	Ephrin type-B receptor 3	6	6	6	pKd	1
Homo sapiens	Ephrin type-B receptor 4	6.1	6.1	6.1	pKd	1
Homo sapiens	Epithelial discoidin domain-containing receptor 1	7.5	7.4	8.4	pIC50	3
Homo sapiens	Epithelial discoidin domain-containing receptor 1	9	9	9	pKd	1
Homo sapiens	Macrophage colony stimulating factor receptor	6.2	6.2	6.2	pIC50	1
Homo sapiens	Macrophage colony stimulating factor receptor	7.4	7.4	7.4	pKd	1
Homo sapiens	MAP kinase p38 alpha	6.3	6.3	6.3	pKd	2
Homo sapiens	MAP kinase p38 beta	7.4	7.4	7.4	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 1	6.1	6.1	6.1	pKd	1
Homo sapiens	Mixed lineage kinase 7	8	8	8	pKd	1
Homo sapiens	Neurotrophic tyrosine kinase receptor type 2	6.3	6.3	6.3	pKd	1
Homo sapiens	NT-3 growth factor receptor	6.2	6.2	6.2	pKd	1
Homo sapiens	Platelet-derived growth factor receptor alpha	7.2	7.2	7.2	pIC50	1
Homo sapiens	Platelet-derived growth factor receptor alpha	6.8	6.8	7.1	pKd	2
Homo sapiens	Platelet-derived growth factor receptor beta	7.2	7.2	7.2	pIC50	2
Homo sapiens	Platelet-derived growth factor receptor beta	7.1	7.1	7.8	pKd	2
Homo sapiens	Serine/threonine-protein kinase 10	5.2	5.2	5.2	pKd	1
Homo sapiens	Serine/threonine-protein kinase B-raf	5.8	5.8	6.2	pKd	2
Homo sapiens	Serine/threonine-protein kinase MRCK beta	6	6	6	pKd	1
Homo sapiens	Serine/threonine-protein kinase RAF	6	6	6	pIC50	1
Homo sapiens	Serine/threonine-protein kinase RAF	5.4	5.4	5.4	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO1	5.3	5.3	5.3	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO3	5.8	5.8	5.8	pKd	1
Homo sapiens	Serine/threonine-protein kinase TNNI3K	6.4	6.4	6.4	pKd	1
Homo sapiens	Stem cell growth factor receptor	6.8	6.7	7.8	pIC50	3
Homo sapiens	Stem cell growth factor receptor	7.3	6.1	7.8	pKd	9
Homo sapiens	Tyrosine-protein kinase ABL	7.5	6.2	7.9	pIC50	10
Homo sapiens	Tyrosine-protein kinase ABL	7.9	6.2	8.4	pKd	15
Homo sapiens	Tyrosine-protein kinase ABL2	7.6	7.6	7.6	pKd	1
Homo sapiens	Tyrosine-protein kinase BLK	6.3	6.3	6.3	pKd	1
Homo sapiens	Tyrosine-protein kinase CSK	5.6	5.6	5.6	pKd	1
Homo sapiens	Tyrosine-protein kinase FGR	6.5	6.5	6.5	pKd	1
Homo sapiens	Tyrosine-protein kinase FRK	7.1	7.1	7.1	pKd	1
Homo sapiens	Tyrosine-protein kinase FYN	5.8	5.8	5.8	pKd	1
Homo sapiens	Tyrosine-protein kinase HCK	6.4	6.4	6.4	pKd	1
Homo sapiens	Tyrosine-protein kinase LCK	7	7	7	pIC50	1
Homo sapiens	Tyrosine-protein kinase LCK	7.3	7.3	7.3	pKd	1
Homo sapiens	Tyrosine-protein kinase Lyn	5.9	5.9	5.9	pIC50	1
Homo sapiens	Tyrosine-protein kinase Lyn	7	7	7	pKd	1
Homo sapiens	Tyrosine-protein kinase receptor FLT3	5	5	5	pIC50	1
Homo sapiens	Tyrosine-protein kinase receptor FLT3	4.4	4.4	4.4	pKd	1
Homo sapiens	Tyrosine-protein kinase receptor RET	6	6	6.1	pKd	2
Homo sapiens	Tyrosine-protein kinase receptor Tie-1	6	6	6	pKd	1
Homo sapiens	Tyrosine-protein kinase SRC	5.7	5.7	5.7	pKd	1
Homo sapiens	Tyrosine-protein kinase TIE-2	6	6	6	pKd	1
Homo sapiens	Tyrosine-protein kinase YES	6	6	6	pKd	1

Kinase-ligand interaction pattern

• Hydrophobic • Aromatic face-to-face • Aromatic face-to-edge • H-bond donor • H-bond acceptor • Ionic positive • Ionic negative

g.l

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

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

•

••

•

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

c.l

VII

VIII

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

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