KLIFS - the structural kinase database

Structure information


PDB:	5AR4
PubMed:	26455654
Release date:	2015-10-21
Resolution:	2.7 Å

Kinase:	RIPK2
Family:	RIPK
Group:	TKL
Species:	HUMAN

Quality Score:	7.6
Missing Residues:	1
Missing Atoms:	0

DFG conformation:	in
αC-helix conformation:	in
Salt bridge K^III.17 and E^αC.24:	Yes (2.9Å)


ASP rotation (xDFG.81) :	289°
PHE rotation (xDFG.82) :	318°
Activation loop position:	-5Å
αC-helix position:	17.7Å

G-rich loop angle:	49.5°
G-rich loop distance:	15.2Å
G-rich loop rotation:	75.2°

Other models from this PDB:

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

I1

H-bond protein

I4

No H-bonds

I10

H-bond ligand

H-bond protein

Binding pocket sequence

Uniprot	RYLSRGASGTVSSVAVKHLDVLREAEILHKARSYILPILGIGIVTEYMPNGSLNELLHRHNMTPPLLHHDLKTQNILLIADFGLS
Structure:	RYLSRGASGTVSSVAVKHLDVLREAEILHKARSYILPILGIGIVTEYMPNGSLNELLHRHNMTPPLLHHDLKTQNILLIADFGL_

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: SB2
Ligand Name: 4-[5-(4-FLUORO-PHENYL)-2-(4-METHANESULFINYL-PHENYL)-3H-IMIDAZOL-4-YL]-PYRIDINE

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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 R
22

2 Y
23

3 L
24

4 S
25

5 R
26

6 G
27

7 A
28

8 S
29

9 G
30

10 T
31

11 V
32

12 S
33

13 S
34

14 V
44

15 A
45

16 V
46

17 K
47

18 H
48

19 L
49

20 D
62

■

αC

b.l

IV

21 V
63

22 L
64

23 R
65

24 E
66

25 A
67

26 E
68

27 I
69

28 L
70

29 H
71

30 K
72

31 A
73

32 R
74

33 S
76

34 Y
77

35 I
78

36 L
79

37 P
80

38 I
81

39 L
82

40 G
83

■

IV

V

GK

hinge

linker

αD

αE

41 I
84

42 G
92

43 I
93

44 V
94

45 T
95

46 E
96

47 Y
97

48 M
98

49 P
99

50 N
100

51 G
101

52 S
102

53 L
103

54 N
104

55 E
105

56 L
106

57 L
107

58 H
108

59 R
109

60 H
136

■

■♦

■▲

αE

VI

c.l

VII

VIII

x

61 N
137

62 M
138

63 T
139

64 P
140

65 P
141

66 L
142

67 L
143

68 H
144

69 H
145

70 D
146

71 L
147

72 K
148

73 T
149

74 Q
150

75 N
151

76 I
152

77 L
153

78 L
154

79 I
162

80 A
163

■

DFG

a.l

81 D
164

82 F
165

83 G
166

84 L
167

85 _
_

■

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL10
Bioaffinities: 251 records for 64 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Activin receptor type-1B	5.5	5.5	5.5	pKd	2
Homo sapiens	Bone morphogenetic protein receptor type-1B	5.5	5.5	5.5	pKd	1
Plasmodium falciparum	Calcium-dependent protein kinase 1	6.1	6.1	6.1	pKd	1
Homo sapiens	Casein kinase I alpha	7.1	7.1	7.1	pKd	1
Homo sapiens	Casein kinase I alpha	6.5	6.5	6.5	pKi	1
Homo sapiens	Casein kinase I delta	6.9	6.9	6.9	pIC50	2
Homo sapiens	Casein kinase I delta	7.4	7.4	7.4	pKd	2
Homo sapiens	Casein kinase I delta	7.4	7.4	7.4	pKi	1
Homo sapiens	Casein kinase I epsilon	7	6.7	7	pKd	3
Homo sapiens	Casein kinase I isoform alpha-like	5.8	5.8	5.8	pKd	2
Homo sapiens	Citron Rho-interacting kinase	6.4	6.4	6.4	pKd	2
Homo sapiens	c-Jun N-terminal kinase 1	6	5.9	6	pKd	3
Homo sapiens	c-Jun N-terminal kinase 1	5.9	5.9	5.9	pKi	1
Homo sapiens	c-Jun N-terminal kinase 2	5.7	5	6.6	pIC50	6
Homo sapiens	c-Jun N-terminal kinase 2	6.9	6.9	7	pKd	3
Homo sapiens	c-Jun N-terminal kinase 2	6.7	6.7	6.7	pKi	1
Homo sapiens	c-Jun N-terminal kinase 3	6.1	6.1	6.5	pIC50	2
Homo sapiens	c-Jun N-terminal kinase 3	7.5	7.4	7.5	pKd	3
Homo sapiens	c-Jun N-terminal kinase 3	7.1	7.1	7.6	pKi	2
Homo sapiens	Discoidin domain-containing receptor 2	5.3	5.3	5.3	pKd	2
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 2	5	5	5	pKd	2
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 5	5.9	5.9	5.9	pKd	1
Homo sapiens	Dual specificity protein kinase TTK	5.6	5.6	5.6	pKd	2
Homo sapiens	Ephrin type-A receptor 6	5.9	5.9	5.9	pKd	2
Homo sapiens	Ephrin type-B receptor 2	5.1	5.1	5.1	pIC50	1
Homo sapiens	Ephrin type-B receptor 2	5.2	5.2	5.2	pKd	1
Homo sapiens	Ephrin type-B receptor 6	5.5	5.5	5.5	pKd	1
Homo sapiens	Epidermal growth factor receptor erbB1	4	4	4	pIC50	1
Homo sapiens	Epidermal growth factor receptor erbB1	5.8	5.5	6.5	pKd	23
Homo sapiens	Epithelial discoidin domain-containing receptor 1	6	6	6	pKd	2
Homo sapiens	Glycogen synthase kinase-3 beta	5.8	5.8	5.8	pKd	2
Homo sapiens	Glycogen synthase kinase-3 beta	5.8	5.8	5.8	pKi	1
Homo sapiens	Hepatocyte growth factor receptor	5.1	5.1	5.1	pKd	1
Homo sapiens	MAP kinase p38 alpha	7.2	7.2	7.2	pEC50	1
Homo sapiens	MAP kinase p38 alpha	7.3	5.2	8	pIC50	50
Homo sapiens	MAP kinase p38 alpha	7.9	7.7	8.4	pKd	5
Homo sapiens	MAP kinase p38 alpha	7.7	7.2	7.8	pKi	3
Mus musculus	MAP kinase p38 alpha	7.7	7.7	7.7	pKd	1
Homo sapiens	MAP kinase p38 beta	6.4	6.3	7.9	pIC50	4
Homo sapiens	MAP kinase p38 beta	7.2	6.6	7.2	pKd	3
Homo sapiens	MAP kinase p38 gamma	5.8	5.8	5.8	pKd	3
Homo sapiens	Misshapen-like kinase 1	5.6	5.6	5.6	pKi	1
Toxoplasma gondii	Mitogen-activated protein kinase 1	7	7	7	pIC50	2
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 4	5.4	5.4	5.4	pKd	2
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 4	6.4	6.4	6.4	pKi	1
Homo sapiens	Mixed lineage kinase 7	5.4	5.4	5.4	pKd	2
Homo sapiens	Phosphatidylinositol-4-phosphate 5-kinase type-1 gamma	5.6	5.6	5.6	pKd	1
Homo sapiens	Receptor protein-tyrosine kinase erbB-2	4.7	4.7	4.7	pIC50	1
Homo sapiens	Receptor protein-tyrosine kinase erbB-4	5.3	5.3	5.3	pKd	1
Homo sapiens	Ribosomal protein S6 kinase alpha 1	6.5	6.5	6.5	pKd	4
Homo sapiens	Ribosomal protein S6 kinase alpha 6	6.6	6.6	6.6	pKd	4
Homo sapiens	Serine/threonine-protein kinase 2	5.4	5.3	5.4	pKd	3
Homo sapiens	Serine/threonine-protein kinase 2	5.7	5.7	5.7	pKi	1
Homo sapiens	Serine/threonine-protein kinase 32A	5.9	5.9	5.9	pKd	1
Homo sapiens	Serine/threonine-protein kinase 32B	5.7	5.7	5.7	pKd	2
Homo sapiens	Serine/threonine-protein kinase 36	5.9	5.9	6.1	pKd	3
Homo sapiens	Serine/threonine-protein kinase B-raf	6.2	6.2	6.3	pKd	4
Homo sapiens	Serine/threonine-protein kinase D2	5.2	5.2	5.2	pKi	1
Homo sapiens	Serine/threonine-protein kinase GAK	6.9	6.9	7	pIC50	2
Homo sapiens	Serine/threonine-protein kinase GAK	7.7	7.4	7.7	pKd	3
Homo sapiens	Serine/threonine-protein kinase MRCK-A	5.2	5.2	5.2	pKd	2
Homo sapiens	Serine/threonine-protein kinase MRCK beta	5.6	5.6	5.6	pKd	2
Homo sapiens	Serine/threonine-protein kinase MRCK gamma	6.4	6.4	6.4	pKd	2
Homo sapiens	Serine/threonine protein kinase NLK	7.6	7.6	7.6	pKd	2
Homo sapiens	Serine/threonine-protein kinase RAF	6.4	5.7	6.5	pIC50	4
Homo sapiens	Serine/threonine-protein kinase RAF	6	6	6	pKd	2
Homo sapiens	Serine/threonine-protein kinase RIPK2	6.6	5.2	8	pIC50	7
Homo sapiens	Serine/threonine-protein kinase RIPK2	7.6	5.7	7.6	pKd	3
Homo sapiens	Serine/threonine-protein kinase SIK2	6	6	6	pKi	1
Homo sapiens	Serine/threonine-protein kinase SIK3	5.4	5.4	5.4	pKd	1
Homo sapiens	Serine/threonine-protein kinase TNNI3K	5.5	5.5	5.5	pKd	2
Homo sapiens	TGF-beta receptor type I	4.5	4.5	5.2	pIC50	2
Homo sapiens	TGF-beta receptor type I	5.2	5.2	5.2	pKd	2
Homo sapiens	TGF-beta receptor type II	5.8	5.8	5.8	pKd	2
Homo sapiens	TRAF2- and NCK-interacting kinase	6.1	5.8	6.1	pKd	3
Homo sapiens	Tyrosine-protein kinase ABL	5.4	5.4	5.6	pKd	2
Homo sapiens	Tyrosine-protein kinase BRK	5.4	5.1	5.4	pKd	3
Homo sapiens	Tyrosine-protein kinase FRK	5.8	5.4	5.8	pKd	3
Homo sapiens	Tyrosine-protein kinase FRK	6.6	6.6	6.6	pKi	1
Homo sapiens	Tyrosine-protein kinase LCK	5.5	5.5	5.5	pIC50	1
Homo sapiens	Tyrosine-protein kinase LCK	5.6	5.6	5.6	pKd	2
Homo sapiens	Tyrosine-protein kinase LCK	5.3	5.3	5.3	pKi	1
Homo sapiens	Tyrosine-protein kinase SRC	5.3	5.3	5.3	pIC50	1
Homo sapiens	Tyrosine-protein kinase SRC	5.3	5.3	5.3	pKd	2
Homo sapiens	Tyrosine-protein kinase TIE-2	4.7	4.7	4.7	pIC50	1
Homo sapiens	Tyrosine-protein kinase TXK	5.4	5.4	5.4	pKd	2
Homo sapiens	Tyrosine-protein kinase TYK2	5.7	5.7	5.7	pKd	2
Homo sapiens	Uncharacterized aarF domain-containing protein kinase 4	5.5	5.5	5.5	pKd	2
Homo sapiens	Vascular endothelial growth factor receptor 3	5.2	5.2	5.2	pKi	1

5AR4 - chain B | Receptor interacting serine/threonine kinase 2