KLIFS - the structural kinase database

Structure information


PDB:	2HIW
PubMed:	16873026
Release date:	2006-08-22
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 (2.8Å)


ASP rotation (xDFG.81) :	194°
PHE rotation (xDFG.82) :	181°
Activation loop position:	2.4Å
αC-helix position:	18.4Å

G-rich loop angle:	54.9°
G-rich loop distance:	16.3Å
G-rich loop rotation:	51.3°

Other models from this PDB:

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

O1

H-bond ligand

Binding pocket sequence

Uniprot	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS
Structure:	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: 7MP
Ligand Name: 7-AMINO-1-METHYL-3-(2-METHYL-5-{[3-(TRIFLUOROMETHYL)BENZOYL]AMINO}PHENYL)-2-OXO-2,3-DIHYDROPYRIMIDO[4,5-D]PYRIMIDIN-1-IUM

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
264

2 K
265

3 L
266

4 G
267

5 G
268

6 G
269

7 Q
270

8 Y
271

9 G
272

10 E
273

11 V
274

12 Y
275

13 E
276

14 V
286

15 A
287

16 V
288

17 K
289

18 T
290

19 L
291

20 E
300

■

αC

b.l

IV

21 F
301

22 L
302

23 K
303

24 E
304

25 A
305

26 A
306

27 V
307

28 M
308

29 K
309

30 E
310

31 I
311

32 K
312

33 P
314

34 N
315

35 L
316

36 V
317

37 Q
318

38 L
319

39 L
320

40 G
321

■

IV

V

GK

hinge

linker

αD

αE

41 V
322

42 Y
330

43 I
331

44 I
332

45 T
333

46 E
334

47 F
335

48 M
336

49 T
337

50 Y
338

51 G
339

52 N
340

53 L
341

54 L
342

55 D
343

56 Y
344

57 L
345

58 R
346

59 E
347

60 Y
371

■

■▲▲

αE

VI

c.l

VII

VIII

x

61 L
372

62 E
373

63 K
374

64 K
375

65 N
376

66 F
377

67 I
378

68 H
379

69 R
380

70 D
381

71 L
382

72 A
383

73 A
384

74 R
385

75 N
386

76 C
387

77 L
388

78 V
389

79 V
397

80 A
398

■

DFG

a.l

81 D
399

82 F
400

83 G
401

84 L
402

85 S
403

■▲

■♦

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL459850
Bioaffinities: 21 records for 20 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Ephrin type-A receptor 3	8.7	8.7	8.7	pEC50	1
Homo sapiens	Ephrin type-B receptor 4	8.4	8.4	8.4	pEC50	1
Homo sapiens	Fibroblast growth factor receptor 1	7.1	7.1	7.1	pEC50	1
Homo sapiens	Fibroblast growth factor receptor 3	7.9	7.9	7.9	pIC50	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 2	7.6	7.6	7.6	pIC50	1
Homo sapiens	NT-3 growth factor receptor	7.5	7.5	7.5	pEC50	1
Homo sapiens	Platelet-derived growth factor receptor alpha	8.4	8.4	8.4	pEC50	1
Homo sapiens	Platelet-derived growth factor receptor beta	8.2	8.2	8.2	pEC50	1
Homo sapiens	Stem cell growth factor receptor	8.4	8.4	8.4	pEC50	1
Homo sapiens	Tyrosine kinase non-receptor protein 2	7.8	7.8	7.8	pIC50	1
Homo sapiens	Tyrosine-protein kinase ABL	5.8	5.8	5.8	pIC50	1
Mus musculus	Tyrosine-protein kinase ABL	6.6	6.6	6.6	pIC50	1
Homo sapiens	Tyrosine-protein kinase BMX	7.5	7.5	7.5	pEC50	1
Homo sapiens	Tyrosine-protein kinase BMX	8.9	8.9	8.9	pIC50	1
Homo sapiens	Tyrosine-protein kinase FES	9	9	9	pIC50	1
Homo sapiens	Tyrosine-protein kinase LCK	8.3	8.3	8.3	pEC50	1
Homo sapiens	Tyrosine-protein kinase receptor RET	7.1	7.1	7.1	pEC50	1
Homo sapiens	Tyrosine-protein kinase SRC	7.9	7.9	7.9	pEC50	1
Homo sapiens	Tyrosine-protein kinase TIE-2	6.7	6.7	6.7	pEC50	1
Homo sapiens	Vascular endothelial growth factor receptor 1	6.6	6.6	6.6	pEC50	1
Homo sapiens	Vascular endothelial growth factor receptor 2	7.7	7.7	7.7	pEC50	1

2HIW - chain B | ABL proto-oncogene 1, non-receptor tyrosine kinase