KLIFS - the structural kinase database

Structure information


PDB:	1YOM
PubMed:	16168436
Release date:	2006-01-27
Resolution:	2.9 Å

Kinase:	SRC
Family:	Src
Group:	TK
Species:	HUMAN

Quality Score:	7.5
Missing Residues:	3
Missing Atoms:	13

DFG conformation:	in
αC-helix conformation:	in
Salt bridge K^III.17 and E^αC.24:	No


ASP rotation (xDFG.81) :	308°
PHE rotation (xDFG.82) :	7°
Activation loop position:	-3.5Å
αC-helix position:	17.3Å

G-rich loop angle:	60°
G-rich loop distance:	18.8Å
G-rich loop rotation:	31°

Other models from this PDB:

2D & 3D views

Binding pocket waters

No waters were found in the defined clusters

Binding pocket sequence

Uniprot	VKLGQGCFGEVWMVAIKTLAFLQEAQVMKKLREKLVQLYAVYIVTEYMSKGSLLDFLKGYVERMNYVHRDLRAANILVVADFGLA
Structure:	VKLGQGCFGEVWMVAIKTLAFLQEAQVMKKLREKLVQLYAVYIVTEYMNKGSLLDFLKGYVERMNYVHRDLRAANILVVADF___

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: P01
Ligand Name: 2-({6-[(3-CHLOROPHENYL)AMINO]-9-ISOPROPYL-9H-PURIN-2-YL}AMINO)-3-METHYLBUTAN-1-OL

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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 V
273

2 K
274

3 L
275

4 G
276

5 Q
277

6 G
278

7 C
279

8 F
280

9 G
281

10 E
282

11 V
283

12 W
284

13 M
285

14 V
294

15 A
295

16 I
296

17 K
297

18 T
298

19 L
299

20 A
308

■

αC

b.l

IV

21 F
309

22 L
310

23 Q
311

24 E
312

25 A
313

26 Q
314

27 V
315

28 M
316

29 K
317

30 K
318

31 L
319

32 R
320

33 E
322

34 K
323

35 L
324

36 V
325

37 Q
326

38 L
327

39 Y
328

40 A
329

■

IV

V

GK

hinge

linker

αD

αE

41 V
330

42 Y
337

43 I
338

44 V
339

45 T
340

46 E
341

47 Y
342

48 M
343

49 N
344

50 K
345

51 G
346

52 S
347

53 L
348

54 L
349

55 D
350

56 F
351

57 L
352

58 K
353

59 G
354

60 Y
378

■

■♦

■▲

■

αE

VI

c.l

VII

VIII

x

61 V
379

62 E
380

63 R
381

64 M
382

65 N
383

66 Y
384

67 V
385

68 H
386

69 R
387

70 D
388

71 L
389

72 R
390

73 A
391

74 A
392

75 N
393

76 I
394

77 L
395

78 V
396

79 V
404

80 A
405

■

DFG

a.l

81 D
406

82 F
407

83 _
_

84 _
_

85 _
_

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL23327
Bioaffinities: 18 records for 10 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Patiria pectinifera	Cdc2	6.3	6.3	7.4	pIC50	2
Saccharomyces cerevisiae S288c	Cell division control protein 28	7.1	7.1	7.1	pIC50	1
Homo sapiens	Cyclin-dependent kinase 1	4.5	4.5	7.3	pIC50	3
Homo sapiens	Cyclin-dependent kinase 2	7.2	7.2	8.4	pIC50	5
Homo sapiens	Dual-specificity tyrosine-phosphorylation regulated kinase 1A	6.5	6.5	6.5	pIC50	1
Homo sapiens	Insulin receptor	5.3	5.3	5.3	pIC50	1
Homo sapiens	MAP kinase ERK1	5.1	5.1	5.1	pIC50	2
Plasmodium falciparum	Protein kinase Pfmrk	4.6	4.6	4.6	pIC50	1
Homo sapiens	Serine/threonine-protein kinase PAK 4	6.9	6.9	6.9	pIC50	1
Homo sapiens	Tyrosine-protein kinase SRC	6.6	6.6	6.6	pIC50	1

1YOM - chain B | SRC proto-oncogene, non-receptor tyrosine kinase