KLIFS - the structural kinase database

Structure information


PDB:	2E2B
PubMed:	17376680
Release date:	2007-05-22
Resolution:	2.2 Å

Kinase:	ABL1
Family:	Abl
Group:	TK
Species:	HUMAN

Quality Score:	7.6
Missing Residues:	0
Missing Atoms:	0

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


ASP rotation (xDFG.81) :	186°
PHE rotation (xDFG.82) :	179°
Activation loop position:	2.1Å
αC-helix position:	18.6Å

G-rich loop angle:	63.2°
G-rich loop distance:	18.6Å
G-rich loop rotation:	18.6°

Other models from this PDB:

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

I1

H-bond protein

I4

H-bond protein

O1

H-bond ligand

Binding pocket sequence

Uniprot	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS
Structure:	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: 406
Ligand Name: N-[3-(4,5'-BIPYRIMIDIN-2-YLAMINO)-4-METHYLPHENYL]-4-{[(3S)-3-(DIMETHYLAMINO)PYRROLIDIN-1-YL]METHYL}-3-(TRIFLUOROMETHYL)BENZAMIDE

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LABELS
KLIFS residue #
Amino Acid
None
COLORS
Interaction types
KLIFS (all res.)
KLIFS (interacting res.)
None
OTHER
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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

■ 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:CHEMBL206834
Bioaffinities: 34 records for 31 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Breakpoint cluster region protein	7.8	7.8	7.8	pKd	2
Homo sapiens	Discoidin domain-containing receptor 2	7.3	7.3	7.3	pKd	1
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 5	4.9	4.9	4.9	pKd	1
Homo sapiens	Ephrin type-A receptor 2	7.1	7.1	7.1	pKd	1
Homo sapiens	Ephrin type-A receptor 4	5.7	5.7	5.7	pKd	1
Homo sapiens	Ephrin type-A receptor 5	6.5	6.5	6.5	pKd	1
Homo sapiens	Ephrin type-B receptor 2	4.3	4.3	4.3	pKd	1
Homo sapiens	Ephrin type-B receptor 3	5.3	5.3	5.3	pKd	1
Homo sapiens	Ephrin type-B receptor 4	5.9	5.9	5.9	pKd	1
Homo sapiens	Epithelial discoidin domain-containing receptor 1	7.9	7.9	7.9	pKd	1
Homo sapiens	Interleukin-1 receptor-associated kinase 1	5.7	5.7	5.7	pKd	1
Homo sapiens	MAP kinase-activated protein kinase 2	6.5	6.5	6.5	pKd	1
Homo sapiens	MAP kinase-activated protein kinase 3	7.6	7.6	7.6	pKd	1
Homo sapiens	MAP kinase p38 alpha	6.3	6.3	6.3	pKd	1
Homo sapiens	MAP kinase p38 beta	5.8	5.8	5.8	pKd	1
Homo sapiens	Mixed lineage kinase 7	7.2	7.2	7.2	pKd	1
Homo sapiens	Myosin light chain kinase, smooth muscle	5.9	5.9	5.9	pKd	1
Homo sapiens	Phosphatidylinositol-5-phosphate 4-kinase type-2 gamma	5.2	5.2	5.2	pKd	1
Homo sapiens	Platelet-derived growth factor receptor beta	5.5	5.5	5.5	pKd	1
Homo sapiens	Receptor-interacting serine/threonine-protein kinase 3	6.3	6.3	6.3	pKd	1
Homo sapiens	Serine/threonine-protein kinase A-Raf	5.5	5.5	5.5	pKd	1
Homo sapiens	Serine/threonine-protein kinase B-raf	6	6	6	pKd	1
Homo sapiens	Serine/threonine-protein kinase RIPK2	5.8	5.8	5.8	pKd	1
Homo sapiens	Tyrosine-protein kinase ABL	7.6	7.6	7.6	pIC50	1
Homo sapiens	Tyrosine-protein kinase ABL	7.6	7.6	7.6	pKd	1
Homo sapiens	Tyrosine-protein kinase ABL2	8	8	8	pKd	1
Homo sapiens	Tyrosine-protein kinase CSK	5.7	5.7	5.7	pKd	1
Homo sapiens	Tyrosine-protein kinase FRK	6.4	6.4	6.4	pKd	1
Homo sapiens	Tyrosine-protein kinase FYN	5.8	5.8	5.8	pKd	1
Homo sapiens	Tyrosine-protein kinase LCK	6.5	6.5	6.5	pKd	1
Homo sapiens	Tyrosine-protein kinase Lyn	8	8	8	pIC50	1
Homo sapiens	Tyrosine-protein kinase Lyn	6.6	6.6	6.6	pKd	1
Homo sapiens	Tyrosine-protein kinase receptor RET	5.6	5.6	5.6	pKd	1

2E2B - chain A | ABL proto-oncogene 1, non-receptor tyrosine kinase