KLIFS - the kinase structures database

Version: 3.2
Updated: 29-Oct-2025

Kinase structure
Kinase:	MAPK9 (JNK2)
Family:	MAPK
Group:	CMGC
Species:	HUMAN
IUPHAR/BPS ID:	1497
PDB:	3NPC
sc-PDB:
KIDFamMap:	Search
Release date:	2010-08-11
PubMed:	20655210
Chain:	B
Orthosteric ligand:	B96

More entries for 3NPC
3NPC	Chain:	A

Structural information
DFG conformation:	out
αC-helix conformation:	in
G-rich loop angle (distance):	61.4° (19Å)
G-rich loop rotation:	45.3°
Quality Score:	7.2
Resolution:	2.35 Å
Missing Residues:	0
Missing Atoms:	0

Ligand binding mode
Pockets	Subpockets	Waters
front gate back	BP-I-A BP-I-B BP-II-out BP-III BP-V	Cluster I3 O2	Ligand No Yes	Protein Yes Yes

Pocket alignment
Uniprot sequence:	KPIGSGAQGIVCAVAVKKLRAYRELVLLKCVNKNIISLLNVYLVMELMD-ANLCQVIHMHLHSAGIIHRDLKPSNIVVILDFGLA
Sequence structure:	KPIGSGAQGIVCAVAVKKLRAYRELVLLKCVNKNIISLLNVYLVMELMD_ANLCQVIHMHLHSAGIIHRDLKPSNIVVILDFGLA

Ligand affinity
ChEMBL ID:	CHEMBL103667
Bioaffinities:	326 records for 91 kinases

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Activin receptor type-1B	4.4	4.4	4.4	pIC50	1
Homo sapiens	Ankyrin repeat and protein kinase domain-containing protein 1	6	6	6	pKd	2
Homo sapiens	CaM kinase II beta	4.4	4.4	4.4	pIC50	1
Homo sapiens	Cell division cycle 2-like protein kinase 6	6.7	6.7	6.7	pKd	2
Homo sapiens	Cell division protein kinase 8	6.7	6.7	6.7	pKd	2
Homo sapiens	Cell division protein kinase 8	6.8	6.8	6.8	pKi	1
Homo sapiens	Citron Rho-interacting kinase	5.7	5.7	5.7	pKd	2
Homo sapiens	c-Jun N-terminal kinase 1	5	5	5	pKd	1
Homo sapiens	c-Jun N-terminal kinase 2	7.6	6.8	8.2	pIC50	7
Homo sapiens	c-Jun N-terminal kinase 2	8.1	8.1	8.3	pKd	4
Homo sapiens	c-Jun N-terminal kinase 2	8.2	8.2	8.2	pKi	1
Homo sapiens	c-Jun N-terminal kinase 3	5.9	5.9	5.9	pIC50	2
Homo sapiens	c-Jun N-terminal kinase 3	7	7	7.2	pKd	4
Homo sapiens	c-Jun N-terminal kinase 3	7.4	7.4	7.4	pKi	1
Homo sapiens	Cyclin-dependent kinase 5	5.7	5.7	6.4	pKd	3
Homo sapiens	Cyclin-dependent kinase 7	5.5	5.5	5.5	pKd	1
Homo sapiens	Discoidin domain-containing receptor 2	7.9	7.2	8	pIC50	3
Homo sapiens	Discoidin domain-containing receptor 2	7.5	7.5	7.7	pKd	5
Homo sapiens	Dual specificity protein kinase TTK	5.5	5.5	5.9	pKd	3
Homo sapiens	Ephrin type-A receptor 1	6.2	6.2	6.2	pIC50	1
Homo sapiens	Ephrin type-A receptor 1	5	5	5	pKd	2
Homo sapiens	Ephrin type-A receptor 2	6.8	6.8	6.8	pIC50	1
Homo sapiens	Ephrin type-A receptor 2	5.2	5.2	5.5	pKd	3
Homo sapiens	Ephrin type-A receptor 3	5.9	5.9	5.9	pIC50	1
Homo sapiens	Ephrin type-A receptor 3	6.1	6.1	6.2	pKd	3
Homo sapiens	Ephrin type-A receptor 4	7.2	7.2	7.2	pIC50	1
Homo sapiens	Ephrin type-A receptor 4	5.5	5.4	5.5	pKd	3
Homo sapiens	Ephrin type-A receptor 5	7.1	7.1	7.1	pIC50	1
Homo sapiens	Ephrin type-A receptor 5	5.9	5.9	5.9	pKd	3
Homo sapiens	Ephrin type-A receptor 6	5.7	5.7	6.4	pKd	3
Homo sapiens	Ephrin type-A receptor 7	6.1	6.1	6.7	pKd	3
Homo sapiens	Ephrin type-A receptor 8	6.6	6.6	6.9	pKd	3
Homo sapiens	Ephrin type-B receptor 1	7	7	7	pIC50	1
Homo sapiens	Ephrin type-B receptor 1	5.3	5.3	5.4	pKd	3
Homo sapiens	Ephrin type-B receptor 2	6.8	6.8	6.8	pIC50	1
Homo sapiens	Ephrin type-B receptor 2	6.4	6.4	6.4	pKd	2
Homo sapiens	Ephrin type-B receptor 3	5	5	5	pIC50	1
Homo sapiens	Ephrin type-B receptor 4	6.1	6.1	6.1	pIC50	1
Homo sapiens	Epidermal growth factor receptor erbB1	5.4	5.4	5.4	pIC50	1
Homo sapiens	Epidermal growth factor receptor erbB1	5.2	5	5.6	pKd	12
Homo sapiens	Epidermal growth factor receptor erbB1	6.7	6.7	6.7	pKi	1
Homo sapiens	Epithelial discoidin domain-containing receptor 1	8.7	8.7	8.7	pKd	3
Homo sapiens	Fibroblast growth factor receptor 1	4.8	4.8	4.8	pIC50	1
Homo sapiens	Fibroblast growth factor receptor 1	5.4	5.4	5.4	pKd	2
Homo sapiens	Fibroblast growth factor receptor 2	4.6	4.6	4.6	pIC50	1
Homo sapiens	Fibroblast growth factor receptor 4	5.2	5.2	5.2	pIC50	1
Homo sapiens	Focal adhesion kinase 1	5.7	5.7	5.7	pIC50	1
Homo sapiens	Focal adhesion kinase 1	5.2	5.2	5.2	pKd	2
Homo sapiens	Leukocyte tyrosine kinase receptor	5.9	5.9	5.9	pKd	2
Homo sapiens	Macrophage colony stimulating factor receptor	5.1	5.1	5.1	pKd	2
Homo sapiens	MAP kinase ERK2	5	5	5	pIC50	1
Homo sapiens	MAP kinase-interacting serine/threonine-protein kinase MNK1	5.2	5.2	5.2	pKd	1
Homo sapiens	MAP kinase p38 alpha	7.7	6.4	10	pIC50	18
Homo sapiens	MAP kinase p38 alpha	9.6	7.9	10.3	pKd	14
Homo sapiens	MAP kinase p38 alpha	8.1	7.7	10	pKi	4
Mus musculus	MAP kinase p38 alpha	10.3	10.3	10.3	pKd	1
Homo sapiens	MAP kinase p38 beta	8.2	8.2	8.2	pIC50	1
Homo sapiens	MAP kinase p38 beta	6.7	5.8	8.1	pKd	3
Homo sapiens	MAP kinase p38 delta	5.7	5.7	6.5	pIC50	2
Homo sapiens	MAP kinase p38 delta	7.1	7.1	7.1	pKd	1
Homo sapiens	MAP kinase p38 delta	7.3	7.3	7.3	pKi	1
Homo sapiens	MAP kinase p38 gamma	6.5	6.5	7.5	pIC50	5
Homo sapiens	MAP kinase p38 gamma	7.9	7.7	8.5	pKd	3
Homo sapiens	MAP kinase p38 gamma	6.3	6.3	6.3	pKi	1
Homo sapiens	MAP kinase signal-integrating kinase 2	5.8	5.8	6	pKd	3
Homo sapiens	MAP/microtubule affinity-regulating kinase 2	4.4	4.4	4.4	pIC50	1
Homo sapiens	Misshapen-like kinase 1	7.4	7.4	7.4	pIC50	1
Homo sapiens	Misshapen-like kinase 1	6.5	6.5	6.5	pKd	1
Homo sapiens	Mitogen-activated protein kinase 15	5.5	5.5	5.5	pKd	2
Homo sapiens	Mitogen-activated protein kinase kinase kinase 7	6.8	6.8	6.8	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 4	7.1	7.1	7.1	pKd	2
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 4	6.8	6.8	6.8	pKi	1
Homo sapiens	Mixed lineage kinase 7	6.1	6.1	6.1	pKd	2
Homo sapiens	Muscle, skeletal receptor tyrosine protein kinase	5.7	5.7	5.7	pKd	2
Homo sapiens	Nerve growth factor receptor Trk-A	6.8	6.8	6.8	pIC50	1
Homo sapiens	Nerve growth factor receptor Trk-A	6	6	6.1	pKd	3
Homo sapiens	Neurotrophic tyrosine kinase receptor type 2	7.3	7.3	7.3	pIC50	1
Homo sapiens	Neurotrophic tyrosine kinase receptor type 2	6.2	6.2	6.2	pKd	2
Homo sapiens	Neurotrophic tyrosine kinase receptor type 2	6.1	6.1	6.1	pKi	1
Homo sapiens	NT-3 growth factor receptor	6.7	6.7	6.7	pKd	2
Homo sapiens	NT-3 growth factor receptor	6.1	6.1	6.1	pKi	1
Homo sapiens	Platelet-derived growth factor receptor alpha	5.9	5.9	5.9	pKd	2
Homo sapiens	Platelet-derived growth factor receptor beta	5.2	5.2	5.2	pIC50	1
Homo sapiens	Platelet-derived growth factor receptor beta	6	6	6	pKd	3
Homo sapiens	Platelet-derived growth factor receptor beta	5.9	5.9	5.9	pKi	1
Homo sapiens	Protein kinase C beta	4.4	4.4	5.2	pIC50	2
Homo sapiens	Protein kinase C delta	5.7	5.7	5.7	pIC50	1
Homo sapiens	Protein tyrosine kinase 2 beta	4.9	4.9	6.4	pIC50	2
Homo sapiens	Protein tyrosine kinase 2 beta	6	6	6	pKd	2
Homo sapiens	Proto-oncogene tyrosine-protein kinase MER	5.4	5.4	5.4	pKd	2
Homo sapiens	Serine/threonine-protein kinase 10	7.9	7.9	8.2	pKd	3
Homo sapiens	Serine/threonine-protein kinase 2	6.8	6.8	7.1	pKd	3
Homo sapiens	Serine/threonine-protein kinase B-raf	7.1	7.1	7.1	pIC50	1
Homo sapiens	Serine/threonine-protein kinase B-raf	5.6	5.6	5.6	pKd	2
Homo sapiens	Serine/threonine-protein kinase Chk2	4.7	4.7	4.7	pIC50	1
Homo sapiens	Serine/threonine-protein kinase D2	5.5	5.5	5.5	pKi	1
Homo sapiens	Serine/threonine-protein kinase MRCK-A	5	5	5	pKd	2
Homo sapiens	Serine/threonine-protein kinase MRCK beta	6	6	6	pKd	2
Homo sapiens	Serine/threonine-protein kinase MRCK gamma	5.9	5.9	5.9	pKd	2
Homo sapiens	Serine/threonine protein kinase NLK	6	6	6	pKd	2
Homo sapiens	Serine/threonine-protein kinase RAF	5.9	5.9	5.9	pIC50	2
Homo sapiens	Serine/threonine-protein kinase RIPK2	5	5	5	pIC50	1
Homo sapiens	Serine/threonine-protein kinase RIPK2	5.2	5.2	5.2	pKd	1
Homo sapiens	Stem cell growth factor receptor	6.6	5.6	6.8	pKd	11
Homo sapiens	TRAF2- and NCK-interacting kinase	6.9	6.9	8	pKd	4
Homo sapiens	Tyrosine-protein kinase ABL	4.4	4.4	4.4	pIC50	1
Homo sapiens	Tyrosine-protein kinase ABL	5.6	5.1	7.4	pKd	18
Mus musculus	Tyrosine-protein kinase ABL	4.8	4.8	4.8	pIC50	1
Homo sapiens	Tyrosine-protein kinase ABL2	5.9	5.9	5.9	pKd	1
Homo sapiens	Tyrosine-protein kinase BLK	6.2	6.2	6.2	pKd	2
Homo sapiens	Tyrosine-protein kinase FER	4.8	4.8	4.8	pIC50	1
Homo sapiens	Tyrosine-protein kinase FGR	5.1	5.1	5.1	pIC50	1
Homo sapiens	Tyrosine-protein kinase FRK	5.9	5.9	6.4	pKd	3
Homo sapiens	Tyrosine-protein kinase FYN	4.6	4.6	4.6	pIC50	1
Homo sapiens	Tyrosine-protein kinase HCK	5.8	5.8	5.8	pIC50	1
Homo sapiens	Tyrosine-protein kinase LCK	4.5	4.5	5.7	pIC50	2
Homo sapiens	Tyrosine-protein kinase LCK	5.9	5.9	6	pKd	3
Homo sapiens	Tyrosine-protein kinase LCK	5.7	5.7	5.7	pKi	1
Homo sapiens	Tyrosine-protein kinase Lyn	6	6	6	pIC50	1
Homo sapiens	Tyrosine-protein kinase Lyn	5.6	5.6	5.6	pKd	2
Homo sapiens	Tyrosine-protein kinase Lyn	6.2	6.2	6.2	pKi	1
Homo sapiens	Tyrosine-protein kinase receptor FLT3	5.6	5.3	6.1	pKd	7
Homo sapiens	Tyrosine-protein kinase receptor RET	7.5	7.5	7.5	pIC50	1
Homo sapiens	Tyrosine-protein kinase receptor RET	6.3	6.3	6.6	pKd	4
Homo sapiens	Tyrosine-protein kinase receptor Tie-1	8.1	8.1	8.1	pKd	2
Homo sapiens	Tyrosine-protein kinase receptor TYRO3	5.7	5.7	5.7	pKi	1
Homo sapiens	Tyrosine-protein kinase SRC	4.5	4.5	4.5	pIC50	1
Homo sapiens	Tyrosine-protein kinase TIE-2	7.6	7.6	7.6	pIC50	1
Homo sapiens	Tyrosine-protein kinase TIE-2	7.7	7.7	8	pKd	3
Homo sapiens	Tyrosine-protein kinase YES	5.1	5.1	5.1	pIC50	1
Homo sapiens	Tyrosine-protein kinase YES	5.3	5.3	5.3	pKd	2
Homo sapiens	Vascular endothelial growth factor receptor 1	6.6	6.6	6.6	pIC50	1
Homo sapiens	Vascular endothelial growth factor receptor 1	6.4	6.4	6.4	pKd	2
Homo sapiens	Vascular endothelial growth factor receptor 1	5.6	5.6	5.6	pKi	1
Homo sapiens	Vascular endothelial growth factor receptor 2	6.5	6.5	6.5	pIC50	1
Homo sapiens	Vascular endothelial growth factor receptor 2	5.4	5.4	5.5	pKd	3
Homo sapiens	Vascular endothelial growth factor receptor 2	6.6	6.6	6.6	pKi	1
Homo sapiens	Vascular endothelial growth factor receptor 3	6.6	6.6	6.6	pIC50	1
Homo sapiens	Vascular endothelial growth factor receptor 3	5.2	5.2	5.6	pKd	3
Homo sapiens	Vascular endothelial growth factor receptor 3	6	6	6	pKi	1

Kinase-ligand interaction pattern

• Hydrophobic • Aromatic face-to-face • Aromatic face-to-edge • H-bond donor • H-bond acceptor • Ionic positive • Ionic negative

g.l

III

αC

1 K
30

2 P
31

3 I
32

4 G
33

5 S
34

6 G
35

7 A
36

8 Q
37

9 G
38

10 I
39

11 V
40

12 C
41

13 A
42

14 V
52

15 A
53

16 V
54

17 K
55

18 K
56

19 L
57

20 R
69

•

αC

b.l

21 A
70

22 Y
71

23 R
72

24 E
73

25 L
74

26 V
75

27 L
76

28 L
77

29 K
78

30 C
79

31 V
80

32 N
81

33 K
83

34 N
84

35 I
85

36 I
86

37 S
87

38 L
88

39 L
89

40 N
90

•

••

•

hinge

linker

αD

αE

41 V
91

42 Y
105

43 L
106

44 V
107

45 M
108

46 E
109

47 L
110

48 M
111

49 D
112

50 _
_

51 A
113

52 N
114

53 L
115

54 C
116

55 Q
117

56 V
118

57 I
119

58 H
120

59 M
121

60 H
141

•

••

αE

c.l

VII

VIII

61 L
142

62 H
143

63 S
144

64 A
145

65 G
146

66 I
147

67 I
148

68 H
149

69 R
150

70 D
151

71 L
152

72 K
153

73 P
154

74 S
155

75 N
156

76 I
157

77 V
158

78 V
159

79 I
167

80 L
168

•

DFG

a.l

81 D
169

82 F
170

83 G
171

84 L
172

85 A
173

••

Interaction pattern search

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