KLIFS - the structural kinase database

Structure information


PDB:	5VD0
PubMed:	28792760
Release date:	2017-08-23
Resolution:	2.13 Å

Kinase:	PKMYT1 (MYT1)
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 (3Å)


ASP rotation (xDFG.81) :	326°
PHE rotation (xDFG.82) :	358°
Activation loop position:	-3.1Å
αC-helix position:	18Å

G-rich loop angle:	56.6°
G-rich loop distance:	17.5Å
G-rich loop rotation:	54.3°

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

I2

H-bond ligand

H-bond protein

I4

H-bond protein

I5

H-bond ligand

H-bond protein

Binding pocket sequence

Uniprot	SRLGHGSYGEVFKYAVKRSRKLAEVGSHEKVGPCCVRLEQAYLQTELC-GPSLQQHCEAHLHSQGLVHLDVKPANIFLLGDFGLL
Structure:	SRLGHGSYGEVFKYAVKRSRKLAEVGSHEKVGPCCVRLEQAYLQTELC_GPSLQQHCEAHLHSQGLVHLDVKPANIFLLGDFGLL

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

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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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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 S
114

2 R
115

3 L
116

4 G
117

5 H
118

6 G
119

7 S
120

8 Y
121

9 G
122

10 E
123

11 V
124

12 F
125

13 K
126

14 Y
136

15 A
137

16 V
138

17 K
139

18 R
140

19 S
141

20 R
153

■

αC

b.l

IV

21 K
154

22 L
155

23 A
156

24 E
157

25 V
158

26 G
159

27 S
160

28 H
161

29 E
162

30 K
163

31 V
164

32 G
165

33 P
168

34 C
169

35 C
170

36 V
171

37 R
172

38 L
173

39 E
174

40 Q
175

■

IV

V

GK

hinge

linker

αD

αE

41 A
176

42 Y
184

43 L
185

44 Q
186

45 T
187

46 E
188

47 L
189

48 C
190

49 _
_

50 G
191

51 P
192

52 S
193

53 L
194

54 Q
195

55 Q
196

56 H
197

57 C
198

58 E
199

59 A
200

60 H
223

■▲

■

■▲▲

■

αE

VI

c.l

VII

VIII

x

61 L
224

62 H
225

63 S
226

64 Q
227

65 G
228

66 L
229

67 V
230

68 H
231

69 L
232

70 D
233

71 V
234

72 K
235

73 P
236

74 A
237

75 N
238

76 I
239

77 F
240

78 L
241

79 L
249

80 G
250

■

■♦

DFG

a.l

81 D
251

82 F
252

83 G
253

84 L
254

85 L
255

■

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

5VD0 - chain A | Protein kinase, membrane associated tyrosine/threonine 1

Structure information

2D & 3D views

Binding pocket waters

Binding pocket sequence

Modified residues

Orthosteric ligand

Kinase-ligand interactions

Interaction pattern search

Binding affinities