KLIFS - the structural kinase database

Structure information


PDB:	5DH3
PubMed:	27535619
Release date:	2016-08-31
Resolution:	2.47 Å

Kinase:	STK3 (MST2)
Family:	STE20
Group:	STE
Species:	HUMAN

Quality Score:	9.1
Missing Residues:	0
Missing Atoms:	9

DFG conformation:	in
αC-helix conformation:	in
Salt bridge K^III.17 and E^αC.24:	Yes (3.2Å)


ASP rotation (xDFG.81) :	10°
PHE rotation (xDFG.82) :	15°
Activation loop position:	-3.6Å
αC-helix position:	18Å

G-rich loop angle:	52.2°
G-rich loop distance:	14.8Å
G-rich loop rotation:	82.5°

Other models from this PDB:

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

I5

H-bond protein

I11

H-bond ligand

Binding pocket sequence

Uniprot	EKLGEGSYGSVFKVAIKQVEIIKEISIMQQCDPYVVKYYGSWIVMEYCGAGSVSDIIRLYLHFMRKIHRDIKAGNILLLADFGVA
Structure:	EKLGEGSYGSVFKVAIKQVEIIKEISIMQQCDPYVVKYYGSWIVMEYCGAGSVSDIIRLYLHFMRKIHRDIKAGNILLLADFGVA

Modified residues

Residue 174 (not in pocket)

Phosphorylated threonine

Residue 180 (not in pocket)

Phosphorylated threonine

Orthosteric ligand

Ligand HET-code: 5BS
Ligand Name: 4-[(5,10-dimethyl-6-oxo-6,10-dihydro-5H-pyrimido[5,4-b]thieno[3,2-e][1,4]diazepin-2-yl)amino]benzenesulfonamide

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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 E
31

2 K
32

3 L
33

4 G
34

5 E
35

6 G
36

7 S
37

8 Y
38

9 G
39

10 S
40

11 V
41

12 F
42

13 K
43

14 V
53

15 A
54

16 I
55

17 K
56

18 Q
57

19 V
58

20 E
66

■

αC

b.l

IV

21 I
67

22 I
68

23 K
69

24 E
70

25 I
71

26 S
72

27 I
73

28 M
74

29 Q
75

30 Q
76

31 C
77

32 D
78

33 P
80

34 Y
81

35 V
82

36 V
83

37 K
84

38 Y
85

39 Y
86

40 G
87

■

IV

V

GK

hinge

linker

αD

αE

41 S
88

42 W
96

43 I
97

44 V
98

45 M
99

46 E
100

47 Y
101

48 C
102

49 G
103

50 A
104

51 G
105

52 S
106

53 V
107

54 S
108

55 D
109

56 I
110

57 I
111

58 R
112

59 L
113

60 Y
136

■

■♦

■▲

■

■▲

αE

VI

c.l

VII

VIII

x

61 L
137

62 H
138

63 F
139

64 M
140

65 R
141

66 K
142

67 I
143

68 H
144

69 R
145

70 D
146

71 I
147

72 K
148

73 A
149

74 G
150

75 N
151

76 I
152

77 L
153

78 L
154

79 L
162

80 A
163

■

DFG

a.l

81 D
164

82 F
165

83 G
166

84 V
167

85 A
168

■

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL4554938

Bioaffinities: No (p)K_i/(p)IC₅₀/(p)EC₅₀ values for kinases found (with a ChEMBL confidence ≥ 8).

5DH3 - chain B (model A) | Serine/threonine kinase 3