KLIFS - the structural kinase database

Structure information


PDB:	6NCG
PubMed:	-
Release date:	2019-01-16
Resolution:	2.45 Å

Kinase:	VRK2
Family:	VRK
Group:	CK1
Species:	HUMAN

Quality Score:	6.4
Missing Residues:	4
Missing Atoms:	38

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


ASP rotation (xDFG.81) :	352°
PHE rotation (xDFG.82) :	15°
Activation loop position:	-3.5Å
αC-helix position:	17.9Å

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	KKIGSGGFGLIYLHVVKVEPLFSELKFYQRVALGIPLFYGSFMVMERLG-IDLQKISGQYIHENEYVHGDIKAANLLLLADYGLS
Structure:	KKIGS__FGLIYLHVVKVEPLFSELKFYQRVALGIPLFYGSFMVMERLG_IDLQKIS__YIHENEYVHGDIKAANLLLLADYGLS

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: KJD
Ligand Name: 4-[6-amino-5-(3,5-difluoro-4-hydroxyphenyl)pyridin-3-yl]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 K
33

2 K
34

3 I
35

4 G
36

5 S
37

6 _
_

7 _
_

8 F
40

9 G
41

10 L
42

11 I
43

12 Y
44

13 L
45

14 H
58

15 V
59

16 V
60

17 K
61

18 V
62

19 E
63

20 P
69

■

αC

b.l

IV

21 L
70

22 F
71

23 S
72

24 E
73

25 L
74

26 K
75

27 F
76

28 Y
77

29 Q
78

30 R
79

31 V
80

32 A
81

33 L
98

34 G
99

35 I
100

36 P
101

37 L
102

38 F
103

39 Y
104

40 G
105

IV

V

GK

hinge

linker

αD

αE

41 S
106

42 F
118

43 M
119

44 V
120

45 M
121

46 E
122

47 R
123

48 L
124

49 G
125

50 _
_

51 I
126

52 D
127

53 L
128

54 Q
129

55 K
130

56 I
131

57 S
132

58 _
_

59 _
_

60 Y
156

■

▲

■▲

αE

VI

c.l

VII

VIII

x

61 I
157

62 H
158

63 E
159

64 N
160

65 E
161

66 Y
162

67 V
163

68 H
164

69 G
165

70 D
166

71 I
167

72 K
168

73 A
169

74 A
170

75 N
171

76 L
172

77 L
173

78 L
174

79 L
184

80 A
185

■

DFG

a.l

81 D
186

82 Y
187

83 G
188

84 L
189

85 S
190

■

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL4467571
Bioaffinities: 1 record for 1 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Serine/threonine-protein kinase VRK2	6.4	6.4	6.4	pKd	1

6NCG - chain A | Vaccinia related kinase 2