KLIFS - the structural kinase database

Structure information


PDB:	5NXC
PubMed:	-
Release date:	2017-05-24
Resolution:	2.25 Å

Kinase:	LIMK1
Family:	LISK
Group:	TKL
Species:	HUMAN

Quality Score:	6.8
Missing Residues:	3
Missing Atoms:	23

DFG conformation:	in
αC-helix conformation:	out
Salt bridge K^III.17 and E^αC.24:	No (16.3Å)


ASP rotation (xDFG.81) :	307°
PHE rotation (xDFG.82) :	324°
Activation loop position:	-5Å
αC-helix position:	21.9Å

G-rich loop angle:	48.7°
G-rich loop distance:	14.4Å
G-rich loop rotation:	51.8°

2D & 3D views

Binding pocket waters

No waters were found in the defined clusters

Binding pocket sequence

Uniprot	EVLGKGCFGQAIKMVMKELTFLKEVKVMRCLEPNVLKFIGVNFITEYIKGGTLRGIIKSYLHSMNIIHRDLNSHNCLVVADFGLA
Structure:	EVLGKGCFGQAIKMVMKELTFLKEVKVMRCLEPNVLKFIGVNFITEYIKGGTLRGIIKSYLHSMNIIHRDLNSHNCLVVADF___

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: 9DB
Ligand Name: (2~{R})-2-azanyl-2-cyclohexyl-~{N}-[2-(1-methylpyrazol-4-yl)-9-oxidanylidene-3,10,11-triazatricyclo[6.4.1.0^{4,13}]trideca-1,4,6,8(13),11-pentaen-6-yl]ethanamide

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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 E
343

2 V
344

3 L
345

4 G
346

5 K
347

6 G
348

7 C
349

8 F
350

9 G
351

10 Q
352

11 A
353

12 I
354

13 K
355

14 M
365

15 V
366

16 M
367

17 K
368

18 E
369

19 L
370

20 T
380

■

■▲

■

■▲

αC

b.l

IV

21 F
381

22 L
382

23 K
383

24 E
384

25 V
385

26 K
386

27 V
387

28 M
388

29 R
389

30 C
390

31 L
391

32 E
392

33 P
394

34 N
395

35 V
396

36 L
397

37 K
398

38 F
399

39 I
400

40 G
401

■

IV

V

GK

hinge

linker

αD

αE

41 V
402

42 N
410

43 F
411

44 I
412

45 T
413

46 E
414

47 Y
415

48 I
416

49 K
417

50 G
418

51 G
419

52 T
420

53 L
421

54 R
422

55 G
423

56 I
424

57 I
425

58 K
426

59 S
427

60 Y
450

▲

■

■▲

■

αE

VI

c.l

VII

VIII

x

61 L
451

62 H
452

63 S
453

64 M
454

65 N
455

66 I
456

67 I
457

68 H
458

69 R
459

70 D
460

71 L
461

72 N
462

73 S
463

74 H
464

75 N
465

76 C
466

77 L
467

78 V
468

79 V
476

80 A
477

■

DFG

a.l

81 D
478

82 F
479

83 _
_

84 _
_

85 _
_

■▲

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL3990456
Bioaffinities: 17 records for 11 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Fibroblast growth factor receptor 3	7.6	7.6	7.6	pIC50	1
Homo sapiens	LIM domain kinase 1	6.4	6.1	6.8	pIC50	3
Homo sapiens	LIM domain kinase 2	5.5	5.5	6.6	pIC50	2
Homo sapiens	Macrophage colony stimulating factor receptor	8	8	8	pIC50	1
Homo sapiens	Serine/threonine-protein kinase Aurora-A	7.6	7.6	7.6	pIC50	1
Homo sapiens	Serine/threonine-protein kinase Chk1	7.4	7.4	7.4	pEC50	1
Homo sapiens	Serine/threonine-protein kinase Chk1	8.3	8.3	8.3	pIC50	1
Homo sapiens	Serine/threonine-protein kinase Chk1	9.3	9.3	9.3	pKi	1
Homo sapiens	Serine/threonine-protein kinase Chk2	7.4	7.4	7.4	pEC50	1
Homo sapiens	Serine/threonine-protein kinase Chk2	7.3	7.3	7.3	pKi	1
Homo sapiens	Tyrosine-protein kinase receptor FLT3	7.6	7.6	7.6	pIC50	1
Homo sapiens	Tyrosine-protein kinase receptor RET	7.4	7.4	7.4	pIC50	1
Homo sapiens	Tyrosine-protein kinase YES	7.9	7.9	7.9	pIC50	1
Homo sapiens	Vascular endothelial growth factor receptor 2	8.1	8.1	8.1	pIC50	1

5NXC - chain L | LIM domain kinase 1