KLIFS - the structural kinase database

Structure information


PDB:	5VDK
PubMed:	28792760
Release date:	2017-08-23
Resolution:	2.7 Å

Kinase:	WEE2 (Wee1B)
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 (2.3Å)


ASP rotation (xDFG.81) :	335°
PHE rotation (xDFG.82) :	342°
Activation loop position:	-3.2Å
αC-helix position:	17.4Å

G-rich loop angle:	55.3°
G-rich loop distance:	16.1Å
G-rich loop rotation:	73.1°

2D & 3D views

Binding pocket waters

No waters were found in the defined clusters

Binding pocket sequence

Uniprot	EKIGVGEFGTVYKYAIKRSSALHEVYAHAVLGPHVVRYYSSIIQNEYCNGGSLQAAISEYIHNSSMVHLDIKPSNIFIIGDLGHA
Structure:	EKIGVGEFGTVYKYAIKRSSALHEVYAHAVLGPHVVRYYSSIIQNEYCNGGSLQAAISEYIHNSSMVHLDIKPSNIFIIGDLGHA

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: 8X7
Ligand Name: 1-[6-(2-hydroxypropan-2-yl)pyridin-2-yl]-6-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one

Download image
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
216

2 K
217

3 I
218

4 G
219

5 V
220

6 G
221

7 E
222

8 F
223

9 G
224

10 T
225

11 V
226

12 Y
227

13 K
228

14 Y
238

15 A
239

16 I
240

17 K
241

18 R
242

19 S
243

20 S
255

■

αC

b.l

IV

21 A
256

22 L
257

23 H
258

24 E
259

25 V
260

26 Y
261

27 A
262

28 H
263

29 A
264

30 V
265

31 L
266

32 G
267

33 P
270

34 H
271

35 V
272

36 V
273

37 R
274

38 Y
275

39 Y
276

40 S
277

■

IV

V

GK

hinge

linker

αD

αE

41 S
278

42 I
286

43 I
287

44 Q
288

45 N
289

46 E
290

47 Y
291

48 C
292

49 N
293

50 G
294

51 G
295

52 S
296

53 L
297

54 Q
298

55 A
299

56 A
300

57 I
301

58 S
302

59 E
303

60 Y
329

■

■▲

■

■♦

■▲▲

■

αE

VI

c.l

VII

VIII

x

61 I
330

62 H
331

63 N
332

64 S
333

65 S
334

66 M
335

67 V
336

68 H
337

69 L
338

70 D
339

71 I
340

72 K
341

73 P
342

74 S
343

75 N
344

76 I
345

77 F
346

78 I
347

79 I
378

80 G
379

■♦♦

DFG

a.l

81 D
380

82 L
381

83 G
382

84 H
383

85 A
384

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL1976040
Bioaffinities: 58 records for 36 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Breakpoint cluster region protein	5.7	5.7	5.7	pKd	2
Homo sapiens	Casein kinase I alpha	5.4	5.4	5.4	pKi	1
Homo sapiens	Casein kinase II alpha (prime)	6.4	6.4	6.4	pKd	1
Homo sapiens	Cyclin-dependent kinase 5	6.2	6.2	6.2	pKi	1
Homo sapiens	Dual specificity protein kinase CLK4	6	6	6	pKi	1
Homo sapiens	Ephrin type-B receptor 6	6.5	6.5	6.5	pKd	1
Homo sapiens	Focal adhesion kinase 1	5.3	5.3	5.3	pKi	1
Homo sapiens	Inhibitor of nuclear factor kappa B kinase epsilon subunit	5.7	5.7	5.7	pKd	1
Homo sapiens	Inhibitor of nuclear factor kappa B kinase epsilon subunit	5.8	5.8	5.8	pKi	1
Homo sapiens	Leucine-rich repeat serine/threonine-protein kinase 2	6.4	6.4	6.4	pKi	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 11	5.7	5.7	5.7	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 4	7.3	7.3	7.3	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 4	5.8	5.8	5.8	pKi	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 5	6	6	6	pKi	1
Homo sapiens	Protein kinase C nu	6	6	6	pKi	1
Homo sapiens	Protein kinase C theta	6.1	6.1	6.1	pKi	1
Homo sapiens	Serine/threonine-protein kinase GAK	6.4	6.4	6.4	pKd	1
Homo sapiens	Serine/threonine-protein kinase NEK2	6.1	6.1	6.1	pKi	1
Homo sapiens	Serine/threonine-protein kinase Nek3	6.1	6.1	6.1	pKd	1
Homo sapiens	Serine/threonine-protein kinase PAK 4	5.6	5.6	5.6	pKi	1
Homo sapiens	Serine/threonine-protein kinase PCTAIRE-1	5.6	5.6	5.6	pKd	1
Homo sapiens	Serine/threonine-protein kinase PLK1	6.5	6.5	6.5	pIC50	1
Homo sapiens	Serine/threonine-protein kinase PLK1	8.5	8.5	8.5	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO1	6	6	6	pKi	1
Homo sapiens	Serine/threonine-protein kinase TBK1	5.8	5.8	5.8	pKd	1
Homo sapiens	Serine/threonine-protein kinase TBK1	6	6	6	pKi	1
Homo sapiens	Serine/threonine-protein kinase WEE1	7	7	8.3	pIC50	2
Homo sapiens	Serine/threonine-protein kinase WEE1	7.9	7.9	8.5	pKd	3
Homo sapiens	Serine/threonine-protein kinase WNK3	5.6	5.6	5.6	pIC50	1
Homo sapiens	Tyrosine- and threonine-specific cdc2-inhibitory kinase	5.3	5.3	5.9	pIC50	2
Homo sapiens	Tyrosine- and threonine-specific cdc2-inhibitory kinase	5.8	5.8	6.5	pKd	2
Homo sapiens	Tyrosine- and threonine-specific cdc2-inhibitory kinase	6.2	6.2	6.3	pKi	2
Homo sapiens	Tyrosine kinase non-receptor protein 2	6.3	6.3	6.3	pKi	1
Homo sapiens	Tyrosine-protein kinase ABL	5.5	5.5	7.4	pKd	2
Homo sapiens	Tyrosine-protein kinase ABL	6.5	6.5	6.5	pKi	1
Homo sapiens	Tyrosine-protein kinase FYN	5.8	5.8	5.8	pKi	1
Homo sapiens	Tyrosine-protein kinase JAK2	7	7	7	pKd	2
Homo sapiens	Tyrosine-protein kinase JAK2	5.9	5.9	5.9	pKi	2
Homo sapiens	Tyrosine-protein kinase JAK3	7.6	7.6	7.6	pKd	2
Homo sapiens	Tyrosine-protein kinase JAK3	5.9	5.9	5.9	pKi	2
Homo sapiens	Tyrosine-protein kinase LCK	6.4	6.4	6.4	pKi	1
Homo sapiens	Tyrosine-protein kinase receptor TYRO3	5.7	5.7	5.7	pKi	1
Homo sapiens	Tyrosine-protein kinase SYK	6.7	6.7	6.7	pKi	1
Homo sapiens	Uncharacterized aarF domain-containing protein kinase 1	5.7	5.7	5.7	pKd	1
Homo sapiens	Wee1-like protein kinase 2	7.6	7.6	8.4	pKd	2

5VDK - chain A | WEE1 homolog 2 (S. pombe)