KLIFS - the structural kinase database

Structure information


PDB:	5VC6
PubMed:	28792760
Release date:	2017-08-23
Resolution:	2 Å

Kinase:	WEE1 (Wee1)
Family:	WEE
Group:	Other
Species:	HUMAN

Quality Score:	8
Missing Residues:	0
Missing Atoms:	0

DFG conformation:	in
αC-helix conformation:	in
Salt bridge K^III.17 and E^αC.24:	Yes (2.9Å)


ASP rotation (xDFG.81) :	344°
PHE rotation (xDFG.82) :	339°
Activation loop position:	-3.2Å
αC-helix position:	17.6Å

G-rich loop angle:	59.2°
G-rich loop distance:	17.7Å
G-rich loop rotation:	47.5°

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

I2

No H-bonds

I5

H-bond protein

Binding pocket sequence

Uniprot	EKIGSGEFGSVFKYAIKRSNALREVYAHAVLGSHVVRYFSALIQNEYCNGGSLADAISEYIHSMSLVHMDIKPSNIFIIGDLGHV
Structure:	EKIGSGEFGSVFKYAIKRSNALREVYAHAVLGSHVVRYFSALIQNEYCNGGSLADAISEYIHSMSLVHMDIKPSNIFIIGDLGHV

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: P48
Ligand Name: N,1,4,4-TETRAMETHYL-8-{[4-(4-METHYLPIPERAZIN-1-YL)PHENYL]AMINO}-4,5-DIHYDRO-1H-PYRAZOLO[4,3-H]QUINAZOLINE-3-CARBOXAMIDE

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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 E
303

2 K
304

3 I
305

4 G
306

5 S
307

6 G
308

7 E
309

8 F
310

9 G
311

10 S
312

11 V
313

12 F
314

13 K
315

14 Y
325

15 A
326

16 I
327

17 K
328

18 R
329

19 S
330

20 N
342

■

■▲

αC

b.l

IV

21 A
343

22 L
344

23 R
345

24 E
346

25 V
347

26 Y
348

27 A
349

28 H
350

29 A
351

30 V
352

31 L
353

32 G
354

33 S
357

34 H
358

35 V
359

36 V
360

37 R
361

38 Y
362

39 F
363

40 S
364

■

IV

V

GK

hinge

linker

αD

αE

41 A
365

42 L
373

43 I
374

44 Q
375

45 N
376

46 E
377

47 Y
378

48 C
379

49 N
380

50 G
381

51 G
382

52 S
383

53 L
384

54 A
385

55 D
386

56 A
387

57 I
388

58 S
389

59 E
390

60 Y
416

■

■♦

■▲▲

■

αE

VI

c.l

VII

VIII

x

61 I
417

62 H
418

63 S
419

64 M
420

65 S
421

66 L
422

67 V
423

68 H
424

69 M
425

70 D
426

71 I
427

72 K
428

73 P
429

74 S
430

75 N
431

76 I
432

77 F
433

78 I
434

79 I
461

80 G
462

■♦

■

DFG

a.l

81 D
463

82 L
464

83 G
465

84 H
466

85 V
467

■

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL564829
Bioaffinities: 98 records for 87 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Activin receptor type-1	6.3	6.3	6.3	pKd	1
Homo sapiens	Adaptor-associated kinase	5.1	5.1	5.1	pKd	1
Homo sapiens	Breakpoint cluster region protein	6.2	6.2	6.2	pKd	2
Homo sapiens	CaM-kinase kinase beta	5.9	5.9	5.9	pKd	1
Homo sapiens	Casein kinase I alpha	6	6	6	pKd	1
Homo sapiens	Casein kinase I delta	6.6	6.6	6.6	pKd	1
Homo sapiens	Casein kinase I epsilon	6.4	6.4	6.4	pKd	1
Homo sapiens	Casein kinase II alpha (prime)	5.5	5.5	5.5	pKd	1
Homo sapiens	Chaperone activity of bc1 complex-like, mitochondrial	5.5	5.5	5.5	pKd	1
Homo sapiens	c-Jun N-terminal kinase 3	5.6	5.6	5.6	pKd	1
Homo sapiens	Cyclin-dependent kinase 2	7.4	6.4	7.4	pIC50	3
Homo sapiens	Cyclin-dependent kinase 2	6.1	6.1	6.1	pKd	1
Homo sapiens	Cyclin-dependent kinase 4	5.4	5.4	5.4	pKd	1
Homo sapiens	Cyclin-dependent kinase 5	5.9	5.9	5.9	pKd	1
Homo sapiens	Cyclin-dependent kinase 6	5.8	5.8	5.8	pKd	1
Homo sapiens	Cyclin-dependent kinase 7	6.5	6.5	6.5	pKd	1
Homo sapiens	Discoidin domain-containing receptor 2	5.4	5.4	5.4	pKd	1
Homo sapiens	Dual specificity protein kinase CLK4	7.8	7.8	7.8	pKd	1
Homo sapiens	Dual-specificity tyrosine-phosphorylation regulated kinase 1A	7	7	7	pKd	1
Homo sapiens	Dual specificty protein kinase CLK1	8.1	8.1	8.1	pKd	1
Homo sapiens	Ephrin type-A receptor 2	6.2	6.2	6.2	pKd	1
Homo sapiens	Ephrin type-A receptor 4	5.1	5.1	5.1	pKd	1
Homo sapiens	Ephrin type-A receptor 5	6.8	6.8	6.8	pKd	1
Homo sapiens	Ephrin type-B receptor 2	6.1	6.1	6.1	pKd	1
Homo sapiens	Ephrin type-B receptor 3	5.6	5.6	5.6	pKd	1
Homo sapiens	Ephrin type-B receptor 4	6	6	6	pKd	1
Homo sapiens	Epidermal growth factor receptor erbB1	5.5	5.5	5.5	pIC50	1
Homo sapiens	Epithelial discoidin domain-containing receptor 1	5.4	5.4	5.4	pKd	1
Homo sapiens	Fibroblast growth factor receptor 1	5.9	5.9	5.9	pIC50	1
Homo sapiens	Fibroblast growth factor receptor 1	5.9	5.9	5.9	pKd	1
Homo sapiens	Inhibitor of nuclear factor kappa B kinase epsilon subunit	5.5	5.5	5.5	pKd	1
Homo sapiens	Interleukin-1 receptor-associated kinase 1	5.7	5.7	5.7	pKd	1
Homo sapiens	Interleukin-1 receptor-associated kinase 3	6.5	6.5	6.5	pKd	1
Homo sapiens	Interleukin-1 receptor-associated kinase 4	4.6	4.6	4.6	pKd	1
Homo sapiens	Macrophage-stimulating protein receptor	5.7	5.7	5.7	pKd	1
Homo sapiens	MAP/microtubule affinity-regulating kinase 2	5.6	5.6	5.6	pKd	1
Homo sapiens	Maternal embryonic leucine zipper kinase	5.6	5.6	5.6	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 11	5.6	5.6	5.6	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 4	5.4	5.4	5.4	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 1	6.7	6.7	6.7	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 2	4.9	4.9	4.9	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 3	5.7	5.7	5.7	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 5	5	5	5	pKd	1
Homo sapiens	Mitotic checkpoint serine/threonine-protein kinase BUB1	5.6	5.6	5.6	pKd	1
Homo sapiens	Myosin light chain kinase	6.5	6.5	6.5	pKd	1
Homo sapiens	Nerve growth factor receptor Trk-A	7.3	7.3	7.3	pIC50	1
Homo sapiens	Nerve growth factor receptor Trk-A	5.5	5.5	5.5	pKd	1
Homo sapiens	Non-receptor tyrosine-protein kinase TNK1	5.3	5.3	5.3	pKd	1
Homo sapiens	Phosphatidylinositol-5-phosphate 4-kinase type-2 gamma	5.8	5.8	5.8	pKd	1
Homo sapiens	Phosphorylase kinase gamma subunit 2	4.7	4.7	4.7	pKd	1
Homo sapiens	Platelet-derived growth factor receptor beta	6.3	6.3	6.3	pKd	1
Homo sapiens	Protein kinase C nu	6.9	6.9	6.9	pKd	1
Homo sapiens	Serine/threonine-protein kinase 16	6	6	6	pKd	1
Homo sapiens	Serine/threonine-protein kinase Aurora-A	6	6	6	pIC50	1
Homo sapiens	Serine/threonine-protein kinase Aurora-B	5.4	5.4	5.4	pIC50	1
Homo sapiens	Serine/threonine-protein kinase Aurora-B	5.1	5.1	5.1	pKd	1
Homo sapiens	Serine/threonine-protein kinase c-TAK1	5.5	5.5	5.5	pKd	1
Homo sapiens	Serine/threonine-protein kinase D2	6.8	6.8	6.8	pKd	1
Homo sapiens	Serine/threonine-protein kinase GAK	8.5	8.5	8.5	pKd	1
Homo sapiens	Serine/threonine-protein kinase ICK	6.1	6.1	6.1	pKd	1
Homo sapiens	Serine/threonine-protein kinase LATS1	6.2	6.2	6.2	pKd	1
Homo sapiens	Serine/threonine-protein kinase Nek3	5.6	5.6	5.6	pKd	1
Homo sapiens	Serine/threonine-protein kinase NEK6	6	6	6	pIC50	1
Homo sapiens	Serine/threonine-protein kinase NEK9	4.7	4.7	4.7	pKd	1
Homo sapiens	Serine/threonine-protein kinase PCTAIRE-1	6.3	6.3	6.3	pKd	1
Homo sapiens	Serine/threonine-protein kinase PCTAIRE-2	5.9	5.9	5.9	pKd	1
Homo sapiens	Serine/threonine-protein kinase SIK2	7	7	7	pKd	1
Homo sapiens	Serine/threonine-protein kinase SIK3	6.6	6.6	6.6	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO1	6.5	6.5	6.5	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO2	5.3	5.3	5.3	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO3	5	5	5	pKd	1
Homo sapiens	Serine/threonine-protein kinase TBK1	5.7	5.7	5.7	pKd	1
Homo sapiens	Serine/threonine-protein kinase ULK1	5.8	5.8	5.8	pKd	1
Homo sapiens	Serine/threonine-protein kinase WEE1	7.9	7.9	7.9	pKd	2
Homo sapiens	Stem cell growth factor receptor	6.2	6.2	6.2	pIC50	1
Homo sapiens	TRAF2- and NCK-interacting kinase	5.9	5.9	5.9	pKd	1
Homo sapiens	Tyrosine- and threonine-specific cdc2-inhibitory kinase	6	6	6	pKd	1
Homo sapiens	Tyrosine kinase non-receptor protein 2	6.1	6.1	6.1	pKd	1
Homo sapiens	Tyrosine-protein kinase ABL	6.3	6.3	6.3	pIC50	1
Homo sapiens	Tyrosine-protein kinase ABL	5.9	5.9	5.9	pKd	1
Homo sapiens	Tyrosine-protein kinase ABL2	5.4	5.4	5.4	pKd	1
Homo sapiens	Tyrosine-protein kinase FRK	5.5	5.5	5.5	pKd	1
Homo sapiens	Tyrosine-protein kinase FYN	5.8	5.8	5.8	pKd	1
Homo sapiens	Tyrosine-protein kinase HCK	5.9	5.9	5.9	pKd	1
Homo sapiens	Tyrosine-protein kinase LCK	6.7	6.7	6.7	pIC50	1
Homo sapiens	Tyrosine-protein kinase LCK	6.2	6.2	6.2	pKd	1
Homo sapiens	Tyrosine-protein kinase Lyn	5.5	5.5	5.5	pKd	1
Homo sapiens	Tyrosine-protein kinase receptor FLT3	7.3	7.3	7.3	pKd	1
Homo sapiens	Tyrosine-protein kinase receptor RET	5.7	5.7	5.7	pIC50	1
Homo sapiens	Tyrosine-protein kinase receptor RET	5.9	5.9	5.9	pKd	1
Homo sapiens	Tyrosine-protein kinase SRC	5.3	5.3	5.3	pKd	1
Homo sapiens	Tyrosine-protein kinase YES	5.4	5.4	5.4	pKd	1
Homo sapiens	Vascular endothelial growth factor receptor 3	6	6	6	pIC50	1
Homo sapiens	Wee1-like protein kinase 2	7.6	7.6	7.6	pKd	1

5VC6 - chain A | WEE1 G2 checkpoint kinase