KLIFS - the structural kinase database

Structure information


PDB:	4X7Q
PubMed:	25575657
Release date:	2015-02-11
Resolution:	2.33 Å

Kinase:	PIM2
Family:	PIM
Group:	CAMK
Species:	HUMAN

Quality Score:	7.3
Missing Residues:	2
Missing Atoms:	19

DFG conformation:	in
αC-helix conformation:	in
Salt bridge K^III.17 and E^αC.24:	Yes (2.6Å)


ASP rotation (xDFG.81) :	337°
PHE rotation (xDFG.82) :	9°
Activation loop position:	-3.6Å
αC-helix position:	17.9Å

G-rich loop angle:	49.2°
G-rich loop distance:	15.4Å
G-rich loop rotation:	72.8°

Other models from this PDB:

2D & 3D views

Binding pocket waters

No waters were found in the defined clusters

Binding pocket sequence

Uniprot	PLLGKGGFGTVFAVAIKVITCPLEVALLWKVGPGVIRLLDWMLVLERPLAQDLFDYITEHCHSRGVVHRDIKDENILILIDFGSG
Structure:	PLLGKG_FGTVFAVAIKVI_CPLEVALLWKVGPGVIRLLDWMLVLERPLAQDLFDYITEHCHSRGVVHRDIKDENILILIDFGSG

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: 3YR
Ligand Name: 2-(2,6-difluorophenyl)-N-{4-[(3S)-pyrrolidin-3-yloxy]pyridin-3-yl}-1,3-thiazole-4-carboxamide

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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 P
36

2 L
37

3 L
38

4 G
39

5 K
40

6 G
42

7 _
_

8 F
43

9 G
44

10 T
45

11 V
46

12 F
47

13 A
48

14 V
58

15 A
59

16 I
60

17 K
61

18 V
62

19 I
63

20 _
_

■

■♦

■

■▲

αC

b.l

IV

21 C
80

22 P
81

23 L
82

24 E
83

25 V
84

26 A
85

27 L
86

28 L
87

29 W
88

30 K
89

31 V
90

32 G
91

33 P
97

34 G
98

35 V
99

36 I
100

37 R
101

38 L
102

39 L
103

40 D
104

■

IV

V

GK

hinge

linker

αD

αE

41 W
105

42 M
113

43 L
114

44 V
115

45 L
116

46 E
117

47 R
118

48 P
119

49 L
120

50 A
122

51 Q
123

52 D
124

53 L
125

54 F
126

55 D
127

56 Y
128

57 I
129

58 T
130

59 E
131

60 H
153

■

αE

VI

c.l

VII

VIII

x

61 C
154

62 H
155

63 S
156

64 R
157

65 G
158

66 V
159

67 V
160

68 H
161

69 R
162

70 D
163

71 I
164

72 K
165

73 D
166

74 E
167

75 N
168

76 I
169

77 L
170

78 I
171

79 L
180

80 I
181

■▲

■

DFG

a.l

81 D
182

82 F
183

83 G
184

84 S
185

85 G
186

■

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL3354511
Bioaffinities: 3 records for 3 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Serine/threonine-protein kinase PIM1	8.3	8.3	8.3	pIC50	1
Homo sapiens	Serine/threonine-protein kinase PIM2	7.9	7.9	7.9	pIC50	1
Homo sapiens	Serine/threonine-protein kinase PIM3	8.7	8.7	8.7	pIC50	1

4X7Q - chain B | Pim-2 proto-oncogene, serine/threonine kinase