KLIFS - the structural kinase database

Structure information


PDB:	5MO4
PubMed:	28329763
Release date:	2017-04-05
Resolution:	2.17 Å

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

Quality Score:	8
Missing Residues:	3
Missing Atoms:	8

DFG conformation:	out
αC-helix conformation:	in
Salt bridge K^III.17 and E^αC.24:	Yes (2.8Å)


ASP rotation (xDFG.81) :	190°
PHE rotation (xDFG.82) :	176°
Activation loop position:	2.1Å
αC-helix position:	18.6Å

G-rich loop angle:	63.1°
G-rich loop distance:	19Å
G-rich loop rotation:	16°

Other models from this PDB:

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

I1

H-bond protein

I10

H-bond protein

O1

H-bond ligand

Binding pocket sequence

Uniprot	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS
Structure:	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIIIEFMTYGNLLDYLREYLEKKNFIHRNLAARNCLVVADF___

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: NIL
Ligand Name: Nilotinib

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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
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 I
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 _
_

84 _
_

85 _
_

■▲

■♦

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL255863
Bioaffinities: 136 records for 59 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Breakpoint cluster region protein	6.2	6.2	6.2	pKd	2
Plasmodium falciparum	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	6.5	8.2	pKd	5
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	6.1	6.1	6.6	pKd	2
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	Ephrin type-B receptor 6	6.3	6.3	6.3	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	6.9	6.9	9	pKd	2
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	6.3	pKd	3
Homo sapiens	MAP kinase p38 beta	5.4	5.4	7.4	pKd	2
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 1	6.1	6.1	6.1	pKd	1
Homo sapiens	Mixed lineage kinase 7	6	6	8	pKd	2
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	Phosphatidylinositol-5-phosphate 4-kinase type-2 gamma	5.1	5.1	5.1	pKd	1
Homo sapiens	Phosphorylase kinase gamma subunit 2	6.5	6.5	6.5	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	7.6	pIC50	3
Homo sapiens	Platelet-derived growth factor receptor beta	7.1	7.1	7.8	pKd	2
Homo sapiens	Receptor-interacting serine/threonine-protein kinase 3	5.9	5.9	5.9	pKd	1
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 ILK-1	7.7	7.7	7.7	pKd	1
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	4
Homo sapiens	Stem cell growth factor receptor	7.3	6.1	7.8	pKd	9
Homo sapiens	Tyrosine-protein kinase ABL	7.6	6.2	8.9	pIC50	12
Homo sapiens	Tyrosine-protein kinase ABL	7.9	6.2	8.4	pKd	17
Homo sapiens	Tyrosine-protein kinase ABL2	6.5	6.5	7.6	pKd	2
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	6.3	6.3	7.1	pKd	2
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	5.8	5.8	7	pKd	2
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	pIC50	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

Allosteric ligand

Ligand HET-code: AY7
Ligand Name: asciminib

Binding affinities

Ligand not found in ChEMBL.

5MO4 - chain A (model B) | ABL proto-oncogene 1, non-receptor tyrosine kinase

Structure information

2D & 3D views

Binding pocket waters

Binding pocket sequence

Modified residues

Orthosteric ligand

Kinase-ligand interactions

Interaction pattern search

Binding affinities

Allosteric ligand

Binding affinities