KLIFS - the structural kinase database

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 K^III.17 and E^αC.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

Binding pocket waters

The following waters were found in the defined clusters:

I1

H-bond protein

Binding pocket sequence

Uniprot	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS
Structure:	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRNLAARNCLVVADFGLS

Modified residues

No modified residues identified.

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
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
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

■

Interaction pattern search

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

Binding affinities

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

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Epidermal growth factor receptor erbB1	7.1	7.1	7.1	pIC50	2
Homo sapiens	Fibroblast growth factor receptor 1	7.1	7.1	7.2	pIC50	2
Homo sapiens	MAP kinase p38 alpha	6.9	6.9	6.9	pIC50	1
Mus musculus	Platelet-derived growth factor receptor beta	6.7	6.7	6.7	pIC50	1
Homo sapiens	Stem cell growth factor receptor	6.2	6.2	6.2	pIC50	1
Homo sapiens	Tyrosine-protein kinase ABL	8.6	8.6	8.6	pIC50	1
Gallus gallus	Tyrosine-protein kinase SRC	8.2	8.2	8.2	pIC50	1
Homo sapiens	Tyrosine-protein kinase SRC	7.4	7.4	8.3	pIC50	2

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