KLIFS - the structural kinase database

Structure information


PDB:	3LM5
PubMed:	33215924
Release date:	2010-03-16
Resolution:	2.29 Å

Kinase:	STK17B (DRAK2)
Family:	DAPK
Group:	CAMK
Species:	HUMAN

Quality Score:	9.6
Missing Residues:	0
Missing Atoms:	4

DFG conformation:	in
αC-helix conformation:	in
Salt bridge K^III.17 and E^αC.24:	No (5.7Å)


ASP rotation (xDFG.81) :	342°
PHE rotation (xDFG.82) :	5°
Activation loop position:	-3.4Å
αC-helix position:	17.7Å

G-rich loop angle:	53.5°
G-rich loop distance:	16.6Å
G-rich loop rotation:	43.7°

Other models from this PDB:

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

I1

H-bond protein

I2

H-bond protein

I3

H-bond protein

Binding pocket sequence

Uniprot	KELGRGKFAVVRQYAAKFLEILHEIAVLELAKPRVINLHEVILILEYAAGGEIFSLCLPYLHQNNIVHLDLKPQNILLIVDFGMS
Structure:	KELGRGKFAVVRQYAAKFLEILHEIAVLELAKPRVINLHEVILILEYAAGGEIFSLCLPYLHQNNIVHLDLKPQNILLIVDFGMS

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: QUE
Ligand Name: 3,5,7,3',4'-PENTAHYDROXYFLAVONE

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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 K
37

2 E
38

3 L
39

4 G
40

5 R
41

6 G
42

7 K
43

8 F
44

9 A
45

10 V
46

11 V
47

12 R
48

13 Q
49

14 Y
59

15 A
60

16 A
61

17 K
62

18 F
63

19 L
64

20 E
76

■

αC

b.l

IV

21 I
77

22 L
78

23 H
79

24 E
80

25 I
81

26 A
82

27 V
83

28 L
84

29 E
85

30 L
86

31 A
87

32 K
88

33 P
91

34 R
92

35 V
93

36 I
94

37 N
95

38 L
96

39 H
97

40 E
98

■▲

■

IV

V

GK

hinge

linker

αD

αE

41 V
99

42 I
107

43 L
108

44 I
109

45 L
110

46 E
111

47 Y
112

48 A
113

49 A
114

50 G
115

51 G
116

52 E
117

53 I
118

54 F
119

55 S
120

56 L
121

57 C
122

58 L
123

59 P
124

60 Y
148

■

▲

■

▲

αE

VI

c.l

VII

VIII

x

61 L
149

62 H
150

63 Q
151

64 N
152

65 N
153

66 I
154

67 V
155

68 H
156

69 L
157

70 D
158

71 L
159

72 K
160

73 P
161

74 Q
162

75 N
163

76 I
164

77 L
165

78 L
166

79 I
177

80 V
178

■

DFG

a.l

81 D
179

82 F
180

83 G
181

84 M
182

85 S
183

■▲

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL50
Bioaffinities: 43 records for 31 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	ALK tyrosine kinase receptor	5.5	5.5	5.5	pIC50	1
Homo sapiens	CaM kinase II beta	5.5	5.5	5.5	pIC50	1
Homo sapiens	Casein kinase II alpha	5.9	5.9	5.9	pKi	2
Rattus norvegicus	Cell division protein kinase 5	4.2	4.2	4.2	pEC50	1
Homo sapiens	Cyclin-dependent kinase 1	6.4	6.4	6.4	pIC50	1
Homo sapiens	Cyclin-dependent kinase 2	4.4	4.4	4.4	pIC50	1
Homo sapiens	Cyclin-dependent kinase 6	4.6	4.6	4.6	pIC50	2
Homo sapiens	Death-associated protein kinase 1	5.1	5.1	5.1	pIC50	1
Homo sapiens	Epidermal growth factor receptor erbB1	4.8	4.8	6.1	pIC50	2
Homo sapiens	Focal adhesion kinase 1	5.9	5.9	5.9	pIC50	1
Homo sapiens	Glycogen synthase kinase-3 beta	5.7	5.7	5.7	pIC50	1
Homo sapiens	Hepatocyte growth factor receptor	6.2	6.2	6.2	pIC50	1
Homo sapiens	Insulin-like growth factor I receptor	6.5	6.5	6.5	pIC50	1
Homo sapiens	NUAK family SNF1-like kinase 1	5.3	5.3	5.3	pIC50	1
Homo sapiens	PI3-kinase p110-gamma subunit	4.9	4.9	4.9	pIC50	1
Homo sapiens	Protein kinase N1	5.2	5.2	5.2	pIC50	1
Homo sapiens	Serine/threonine-protein kinase AKT	5.3	5.3	5.3	pIC50	1
Homo sapiens	Serine/threonine-protein kinase Aurora-B	6	6	6	pIC50	1
Homo sapiens	Serine/threonine-protein kinase B-raf	5.1	5.1	5.1	pIC50	1
Homo sapiens	Serine/threonine-protein kinase NEK2	5.2	5.2	5.2	pIC50	1
Homo sapiens	Serine/threonine-protein kinase NEK6	5.4	5.4	5.4	pIC50	1
Homo sapiens	Serine/threonine-protein kinase PIM1	6	6	7.4	pIC50	4
Homo sapiens	Serine/threonine-protein kinase PIM1	7.6	7.6	7.6	pKd	1
Homo sapiens	Serine/threonine-protein kinase PLK1	4.2	4.2	5.2	pIC50	2
Homo sapiens	Tyrosine-protein kinase LCK	4.9	4.9	4.9	pIC50	2
Homo sapiens	Tyrosine-protein kinase receptor FLT3	6.2	6.2	6.2	pIC50	1
Homo sapiens	Tyrosine-protein kinase receptor RET	4.1	4.1	4.1	pIC50	1
Homo sapiens	Tyrosine-protein kinase receptor UFO	6	6	6	pIC50	1
Homo sapiens	Tyrosine-protein kinase SRC	4.8	4.8	6.9	pIC50	2
Homo sapiens	Tyrosine-protein kinase SYK	4.5	4.5	4.5	pEC50	1
Homo sapiens	Tyrosine-protein kinase SYK	4.7	4.7	4.7	pIC50	1
Homo sapiens	Tyrosine-protein kinase YES	6.3	6.3	6.3	pKi	1
Homo sapiens	Vascular endothelial growth factor receptor 2	5.8	5.8	6.6	pIC50	2

3LM5 - chain A (model A) | Serine/threonine kinase 17b

Structure information

2D & 3D views

Binding pocket waters

Binding pocket sequence

Modified residues

Orthosteric ligand

Kinase-ligand interactions

Interaction pattern search

Binding affinities