KLIFS - the structural kinase database

Structure information


PDB:	5VCX
PubMed:	28792760
Release date:	2017-08-23
Resolution:	2.7 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 (3.1Å)


ASP rotation (xDFG.81) :	335°
PHE rotation (xDFG.82) :	354°
Activation loop position:	-3Å
αC-helix position:	18.5Å

G-rich loop angle:	58.9°
G-rich loop distance:	18.1Å
G-rich loop rotation:	55.4°

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

I4

H-bond protein

I5

H-bond protein

I6

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: H8H
Ligand Name: N-(5-CHLORO-1,3-BENZODIOXOL-4-YL)-7-[2-(4-METHYLPIPERAZIN-1-YL)ETHOXY]-5-(TETRAHYDRO-2H-PYRAN-4-YLOXY)QUINAZOLIN-4-AMINE

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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 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:CHEMBL217092
Bioaffinities: 83 records for 51 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Activin receptor type-1	8.4	8.4	8.4	pKd	1
Homo sapiens	Activin receptor type-1B	6.9	6.9	6.9	pKd	1
Homo sapiens	Activin receptor type-2B	5.4	5.4	5.4	pKd	1
Homo sapiens	Bone morphogenetic protein receptor type-1A	7.2	7.2	7.2	pKd	1
Homo sapiens	Bone morphogenetic protein receptor type-1B	7.5	7.5	7.5	pKd	1
Homo sapiens	Breakpoint cluster region protein	7.8	7.8	7.8	pKd	2
Homo sapiens	Chaperone activity of bc1 complex-like, mitochondrial	6.6	6.6	6.6	pKd	1
Homo sapiens	Cyclin-dependent kinase 2	5	5	5	pIC50	1
Homo sapiens	Discoidin domain-containing receptor 2	4.4	4.4	4.4	pKd	1
Homo sapiens	Ephrin type-A receptor 1	8	8	8	pKd	1
Homo sapiens	Ephrin type-A receptor 2	6.1	6.1	6.1	pKd	1
Homo sapiens	Ephrin type-A receptor 4	6	6	6	pKd	1
Homo sapiens	Ephrin type-A receptor 5	5.6	5.6	5.6	pKd	1
Homo sapiens	Ephrin type-B receptor 2	5	5	5	pKd	1
Homo sapiens	Ephrin type-B receptor 4	5.4	5.4	5.4	pKd	1
Homo sapiens	Ephrin type-B receptor 6	5.4	5.4	5.4	pKd	1
Homo sapiens	Epidermal growth factor receptor erbB1	5.6	5.6	7.2	pIC50	4
Homo sapiens	Epithelial discoidin domain-containing receptor 1	5.4	5.4	5.4	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 4	6	6	6	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 5	4.6	4.6	4.6	pKd	1
Homo sapiens	Mixed lineage kinase 7	5.5	5.5	5.5	pKd	1
Homo sapiens	Platelet-derived growth factor receptor alpha	5	5	5	pIC50	1
Homo sapiens	Platelet-derived growth factor receptor beta	6.2	6.2	6.2	pKd	1
Homo sapiens	Receptor-interacting serine/threonine-protein kinase 3	5.8	5.8	5.8	pKd	1
Homo sapiens	Serine/threonine-protein kinase 10	4.9	4.9	4.9	pKd	1
Homo sapiens	Serine/threonine-protein kinase 2	4.5	4.5	4.5	pKd	1
Homo sapiens	Serine/threonine-protein kinase GAK	7	7	7	pKd	1
Homo sapiens	Serine/threonine-protein kinase RIPK2	8.7	8.7	8.7	pKd	1
Homo sapiens	Serine/threonine-protein kinase SIK2	5.9	5.9	5.9	pKd	1
Homo sapiens	Serine/threonine-protein kinase SIK3	5.3	5.3	5.3	pKd	1
Homo sapiens	Stem cell growth factor receptor	6.7	6.7	6.7	pIC50	3
Homo sapiens	TGF-beta receptor type I	6.7	6.7	6.7	pKd	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	5	5	6.4	pIC50	2
Homo sapiens	Tyrosine- and threonine-specific cdc2-inhibitory kinase	5.6	5.6	5.6	pKd	1
Homo sapiens	Tyrosine- and threonine-specific cdc2-inhibitory kinase	5.3	5.3	7.4	pKi	2
Homo sapiens	Tyrosine kinase non-receptor protein 2	5.3	5.3	5.3	pKd	1
Homo sapiens	Tyrosine-protein kinase ABL	7.5	7.5	7.5	pIC50	3
Homo sapiens	Tyrosine-protein kinase ABL	7.3	7.3	7.3	pKd	1
Homo sapiens	Tyrosine-protein kinase ABL2	7	7	7	pKd	1
Homo sapiens	Tyrosine-protein kinase BRK	6.3	6.3	6.3	pKd	1
Homo sapiens	Tyrosine-protein kinase BTK	5	5	5	pKd	1
Homo sapiens	Tyrosine-protein kinase CSK	6.1	6.1	6.1	pIC50	3
Homo sapiens	Tyrosine-protein kinase CSK	4.4	4.4	4.4	pKd	1
Homo sapiens	Tyrosine-protein kinase FGR	6	6	6	pKd	1
Homo sapiens	Tyrosine-protein kinase FRK	5.6	5.6	5.6	pKd	1
Homo sapiens	Tyrosine-protein kinase FYN	7	7	7	pKd	1
Homo sapiens	Tyrosine-protein kinase HCK	7	7	7	pKd	1
Homo sapiens	Tyrosine-protein kinase LCK	8.4	8.4	8.4	pIC50	1
Homo sapiens	Tyrosine-protein kinase LCK	8.1	8.1	8.1	pKd	1
Homo sapiens	Tyrosine-protein kinase Lyn	7	7	7	pKd	1
Homo sapiens	Tyrosine-protein kinase receptor FLT3	6.9	6.9	6.9	pKd	1
Homo sapiens	Tyrosine-protein kinase receptor RET	6.8	6.8	6.8	pKd	1
Homo sapiens	Tyrosine-protein kinase SRC	8.6	7.1	9	pIC50	9
Homo sapiens	Tyrosine-protein kinase SRC	6.9	6.9	6.9	pKd	1
Homo sapiens	Tyrosine-protein kinase YES	8.4	8.2	9.2	pIC50	5
Homo sapiens	Tyrosine-protein kinase YES	7	7	7	pKd	1
Homo sapiens	Vascular endothelial growth factor receptor 2	4.7	4.7	4.7	pIC50	2

5VCX - 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