KLIFS - the structural kinase database

Structure information


PDB:	5UKF
PubMed:	28790404
Release date:	2017-03-29
Resolution:	2.4 Å

Kinase:	VRK1
Family:	VRK
Group:	CK1
Species:	HUMAN

Quality Score:	4
Missing Residues:	11
Missing Atoms:	42

DFG conformation:	in
αC-helix conformation:	in
Salt bridge K^III.17 and E^αC.24:	No


ASP rotation (xDFG.81) :	345°
PHE rotation (xDFG.82) :	16°
Activation loop position:	-3.4Å
αC-helix position:	17.6Å

G-rich loop angle:	-
G-rich loop distance:	-
G-rich loop rotation:	-

Other models from this PDB:

2D & 3D views

Binding pocket waters

No waters were found in the defined clusters

Binding pocket sequence

Uniprot	LPIGQGGFGCIYLCVVKVEPLFTELKFYQRAALGVPKYWGSFMIMDRFG-SDLQKIYEAYIHEHEYVHGDIKASNLLLLVDYGLA
Structure:	__________IYL_VVKVEPLFTELKFYQRAALGVPKYWGSFMIMDRFG_SDLQKIYEAYIHEHEYVHGDIKASNLLLLVDYGLA

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: 8E1
Ligand Name: 4-{[(Z)-(7-oxo-6,7-dihydro-8H-[1,3]thiazolo[5,4-e]indol-8-ylidene)methyl]amino}benzene-1-sulfonamide

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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 _
_

2 _
_

3 _
_

4 _
_

5 _
_

6 _
_

7 _
_

8 _
_

9 _
_

10 _
_

11 I
51

12 Y
52

13 L
53

14 _
_

15 V
69

16 V
70

17 K
71

18 V
72

19 E
73

20 P
79

■

αC

b.l

IV

21 L
80

22 F
81

23 T
82

24 E
83

25 L
84

26 K
85

27 F
86

28 Y
87

29 Q
88

30 R
89

31 A
90

32 A
91

33 L
108

34 G
109

35 V
110

36 P
111

37 K
112

38 Y
113

39 W
114

40 G
115

IV

V

GK

hinge

linker

αD

αE

41 S
116

42 F
128

43 M
129

44 I
130

45 M
131

46 D
132

47 R
133

48 F
134

49 G
135

50 _
_

51 S
136

52 D
137

53 L
138

54 Q
139

55 K
140

56 I
141

57 Y
142

58 E
143

59 A
144

60 Y
167

■

▲

■♦▲

■

▲

αE

VI

c.l

VII

VIII

x

61 I
168

62 H
169

63 E
170

64 H
171

65 E
172

66 Y
173

67 V
174

68 H
175

69 G
176

70 D
177

71 I
178

72 K
179

73 A
180

74 S
181

75 N
182

76 L
183

77 L
184

78 L
185

79 L
195

80 V
196

■

DFG

a.l

81 D
197

82 Y
198

83 G
199

84 L
200

85 A
201

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL271595
Bioaffinities: 2 records for 2 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Cyclin-dependent kinase 1	7.5	7.5	7.5	pIC50	1
Homo sapiens	Cyclin-dependent kinase 2	8.6	8.6	8.6	pIC50	1

5UKF - chain B | Vaccinia related kinase 1