KLIFS - the structural kinase database

Structure information


PDB:	2XIK
PubMed:	-
Release date:	2010-07-14
Resolution:	1.97 Å

Kinase:	STK25 (YSK1)
Family:	STE20
Group:	STE
Species:	HUMAN

Quality Score:	9.2
Missing Residues:	0
Missing Atoms:	8

DFG conformation:	in
αC-helix conformation:	in
Salt bridge K^III.17 and E^αC.24:	Yes (4.2Å)


ASP rotation (xDFG.81) :	356°
PHE rotation (xDFG.82) :	14°
Activation loop position:	-3.3Å
αC-helix position:	17.9Å

G-rich loop angle:	53.6°
G-rich loop distance:	15.6Å
G-rich loop rotation:	86.8°

Other models from this PDB:

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

I5

H-bond protein

Binding pocket sequence

Uniprot	DRIGKGSFGEVYKVAIKIIDIQQEITVLSQCDPYITRYFGSWIIMEYLGGGSALDLLKPYLHSERKIHRDIKAANVLLLADFGVA
Structure:	DRIGKGSFGEVYKVAIKIIDIQQEITVLSQCDPYITRYFGSWIIMEYLGGGSALDLLKPYLHSERKIHRDIKAANVLLLADFGVA

Modified residues

Residue 174 (not in pocket)

Phosphorylated threonine

Orthosteric ligand

Ligand HET-code: J60
Ligand Name: 5-[(E)-(5-CHLORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-N-[2-(DIETHYLAMINO)ETHYL]-2,4-DIMETHYL-1H-PYRROLE-3-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 D
24

2 R
25

3 I
26

4 G
27

5 K
28

6 G
29

7 S
30

8 F
31

9 G
32

10 E
33

11 V
34

12 Y
35

13 K
36

14 V
46

15 A
47

16 I
48

17 K
49

18 I
50

19 I
51

20 D
62

■

αC

b.l

IV

21 I
63

22 Q
64

23 Q
65

24 E
66

25 I
67

26 T
68

27 V
69

28 L
70

29 S
71

30 Q
72

31 C
73

32 D
74

33 P
76

34 Y
77

35 I
78

36 T
79

37 R
80

38 Y
81

39 F
82

40 G
83

■

IV

V

GK

hinge

linker

αD

αE

41 S
84

42 W
92

43 I
93

44 I
94

45 M
95

46 E
96

47 Y
97

48 L
98

49 G
99

50 G
100

51 G
101

52 S
102

53 A
103

54 L
104

55 D
105

56 L
106

57 L
107

58 K
108

59 P
109

60 Y
130

■

▲

■

■▲

■

αE

VI

c.l

VII

VIII

x

61 L
131

62 H
132

63 S
133

64 E
134

65 R
135

66 K
136

67 I
137

68 H
138

69 R
139

70 D
140

71 I
141

72 K
142

73 A
143

74 A
144

75 N
145

76 V
146

77 L
147

78 L
148

79 L
156

80 A
157

■

DFG

a.l

81 D
158

82 F
159

83 G
160

84 V
161

85 A
162

■

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL13485
Bioaffinities: 12 records for 7 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Epidermal growth factor receptor erbB1	5.5	5.5	5.5	pIC50	1
Homo sapiens	Fibroblast growth factor receptor 1	6.8	6.8	6.8	pIC50	2
Homo sapiens	Maternal embryonic leucine zipper kinase	6.1	6.1	6.1	pIC50	1
Homo sapiens	Platelet-derived growth factor receptor beta	8.5	5.5	8.5	pIC50	3
Homo sapiens	Serine/threonine-protein kinase NEK2	5.1	5.1	5.1	pIC50	1
Homo sapiens	Stem cell growth factor receptor	8	8	8	pIC50	1
Homo sapiens	Vascular endothelial growth factor receptor 2	7.6	5.5	7.6	pIC50	3

2XIK - chain A (model A) | Serine/threonine kinase 25