KLIFS - the structural kinase database

Structure information


PDB:	4JLC
PubMed:	23746807
Release date:	2013-06-19
Resolution:	3 Å

Kinase:	Tbk1 (TBK1)
Family:	IKK
Group:	Other
Species:	MOUSE

Quality Score:	8
Missing Residues:	0
Missing Atoms:	0

DFG conformation:	in
αC-helix conformation:	out
Salt bridge K^III.17 and E^αC.24:	No (10.9Å)


ASP rotation (xDFG.81) :	339°
PHE rotation (xDFG.82) :	343°
Activation loop position:	-4.2Å
αC-helix position:	22.6Å

G-rich loop angle:	55.6°
G-rich loop distance:	16.4Å
G-rich loop rotation:	50.3°

2D & 3D views

Binding pocket waters

No waters were found in the defined clusters

Binding pocket sequence

Uniprot	DILGQGATANVFRYAVKVFVQMREFEVLKKLNKNIVKLFAIVLIMEFCPCGSLYTVLEEHLRENGIVHRDIKPGNIMRLTDFGAA
Structure:	DILGQGATANVFRYAVKVFVQMREFEVLKKLNKNIVKLFAIVLIMEFCPCGSLYTVLEEHLRENGIVHRDIKPGNIMRLTDFGAA

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: SU6
Ligand Name: 3-{2,4-dimethyl-5-[(Z)-(2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-1H-pyrrol-3-yl}propanoic acid

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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 D
13

2 I
14

3 L
15

4 G
16

5 Q
17

6 G
18

7 A
19

8 T
20

9 A
21

10 N
22

11 V
23

12 F
24

13 R
25

14 Y
35

15 A
36

16 V
37

17 K
38

18 V
39

19 F
40

20 V
51

■

αC

b.l

IV

21 Q
52

22 M
53

23 R
54

24 E
55

25 F
56

26 E
57

27 V
58

28 L
59

29 K
60

30 K
61

31 L
62

32 N
63

33 K
65

34 N
66

35 I
67

36 V
68

37 K
69

38 L
70

39 F
71

40 A
72

■

IV

V

GK

hinge

linker

αD

αE

41 I
73

42 V
83

43 L
84

44 I
85

45 M
86

46 E
87

47 F
88

48 C
89

49 P
90

50 C
91

51 G
92

52 S
93

53 L
94

54 Y
95

55 T
96

56 V
97

57 L
98

58 E
99

59 E
100

60 H
125

■

▲

■

■▲

■

■▲

αE

VI

c.l

VII

VIII

x

61 L
126

62 R
127

63 E
128

64 N
129

65 G
130

66 I
131

67 V
132

68 H
133

69 R
134

70 D
135

71 I
136

72 K
137

73 P
138

74 G
139

75 N
140

76 I
141

77 M
142

78 R
143

79 L
155

80 T
156

■

DFG

a.l

81 D
157

82 F
158

83 G
159

84 A
160

85 A
161

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL274654
Bioaffinities: 51 records for 31 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Adaptor-associated kinase	5.9	5.9	5.9	pKd	1
Homo sapiens	BMP-2-inducible protein kinase	6.5	6.5	6.5	pKd	1
Homo sapiens	Bone morphogenetic protein receptor type-2	7.7	7.7	7.7	pKd	1
Homo sapiens	Casein kinase II alpha (prime)	5.7	5.7	5.7	pKd	1
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 1	5.5	5.5	5.5	pKd	1
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 2	5.5	5.5	5.5	pKd	1
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 5	5.3	5.3	5.3	pKd	1
Homo sapiens	Fibroblast growth factor receptor 1	5.5	5	5.7	pIC50	5
Homo sapiens	Fibroblast growth factor receptor 1	9.5	9.5	9.5	pKd	1
Homo sapiens	Inhibitor of nuclear factor kappa B kinase epsilon subunit	5.8	5.8	5.8	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 11	5.6	5.6	5.6	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 1	5.7	5.7	5.7	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 2	5.6	5.6	5.6	pKd	1
Homo sapiens	Platelet-derived growth factor receptor beta	7.2	4.8	7.3	pIC50	5
Homo sapiens	Platelet-derived growth factor receptor beta	6.1	6.1	6.1	pKd	1
Homo sapiens	Ribosomal protein S6 kinase alpha 1	5.6	5.6	5.6	pKd	2
Homo sapiens	Ribosomal protein S6 kinase alpha 4	5.9	5.9	5.9	pKd	2
Homo sapiens	Ribosomal protein S6 kinase alpha 5	5.5	5.5	5.5	pKd	2
Homo sapiens	Serine/threonine-protein kinase Aurora-A	5.5	5.5	5.5	pKd	1
Homo sapiens	Serine/threonine-protein kinase Aurora-B	7.3	7.3	7.5	pIC50	2
Homo sapiens	Serine/threonine-protein kinase Aurora-B	6	6	6	pKd	1
Homo sapiens	Serine/threonine-protein kinase Aurora-C	6.7	6.7	6.7	pIC50	1
Homo sapiens	Serine/threonine-protein kinase GAK	5.7	5.7	5.7	pKd	1
Homo sapiens	Serine/threonine-protein kinase LATS1	5.5	5.5	5.5	pKd	1
Homo sapiens	Serine/threonine-protein kinase MST1	5.8	5.8	5.8	pKd	1
Homo sapiens	Serine/threonine-protein kinase MST2	5.7	5.7	5.7	pKd	1
Homo sapiens	Serine/threonine-protein kinase TBK1	5.7	5.7	5.7	pKd	1
Homo sapiens	Serine/threonine-protein kinase ULK3	5.8	5.8	5.8	pKd	1
Homo sapiens	TRAF2- and NCK-interacting kinase	7.9	7.9	7.9	pKd	1
Homo sapiens	Tyrosine-protein kinase receptor FLT3	9.1	9.1	9.1	pKd	1
Homo sapiens	Tyrosine-protein kinase receptor RET	6.5	6.5	6.5	pKd	1
Homo sapiens	Tyrosine-protein kinase ZAP-70	4.6	4.6	4.6	pIC50	1
Homo sapiens	Vascular endothelial growth factor receptor 1	7.6	7.6	7.6	pIC50	1
Homo sapiens	Vascular endothelial growth factor receptor 2	5.6	5.4	6.9	pIC50	6

4JLC - chain A | TANK-binding kinase 1