KLIFS - the kinase structures database

Version: 3.2
Updated: 29-Oct-2025

Kinase structure
Kinase:	CDK8
Family:	CDK
Group:	CMGC
Species:	HUMAN
IUPHAR/BPS ID:	1980
PDB:	3RGF
sc-PDB:
KIDFamMap:	Search
Release date:	2011-08-10
PubMed:	21806996
Chain:	A
(Alternate) Model:	A
Orthosteric ligand:	BAX

More entries for 3RGF
3RGF	Alternative model:	B	Chain:	A

Structural information
DFG conformation:	out
αC-helix conformation:	in
G-rich loop angle (distance):	-
G-rich loop rotation:	-
Quality Score:	6
Resolution:	2.2 Å
Missing Residues:	5
Missing Atoms:	0

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

Pocket alignment
Uniprot sequence:	CKVGRGTYGHVYKYALKQISACREIALLRELKPNVISLQKVWLLFDYAE-HDLWHIIKFYLHANWVLHRDLKPANILVIADMGFA
Sequence structure:	CKVG_____HVYKYALKQISACREIALLRELKPNVISLQKVWLLFDYAE_HDLWHIIKFYLHANWVLHRDLKPANILVIADMGFA

Ligand affinity
ChEMBL ID:	CHEMBL1336
Bioaffinities:	631 records for 121 kinases

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Plasmodium falciparum (isolate 3D7)	Calcium-dependent protein kinase 1	6.7	6.7	6.7	pKd	1
Homo sapiens	CaM kinase II beta	5.4	5.4	5.4	pKi	1
Homo sapiens	Casein kinase I alpha	6.6	6.6	6.6	pIC50	1
Homo sapiens	Cell division cycle 2-like protein kinase 6	6.7	6.7	6.7	pIC50	1
Homo sapiens	Cell division cycle 2-like protein kinase 6	6.6	6.6	6.6	pKd	3
Homo sapiens	Cell division protein kinase 8	5.8	5.3	6.7	pIC50	3
Homo sapiens	Cell division protein kinase 8	6.5	6.5	6.5	pKd	3
Homo sapiens	Cell division protein kinase 8	7.1	7.1	7.1	pKi	1
Homo sapiens	Citron Rho-interacting kinase	5.2	5.2	5.2	pKd	3
Homo sapiens	c-Jun N-terminal kinase 2	5.1	5.1	5.4	pKd	2
Homo sapiens	Cyclin-dependent kinase 2	5.1	5.1	5.1	pKd	1
Homo sapiens	Cyclin-dependent kinase 3	5.4	5.4	5.4	pKd	1
Homo sapiens	Cyclin-dependent kinase 5	5.1	5.1	5.2	pKd	2
Homo sapiens	Cyclin-dependent kinase 7	6.9	6.9	6.9	pKd	3
Homo sapiens	Cyclin-dependent kinase-like 2	6.9	6.9	6.9	pKd	2
Homo sapiens	Cyclin-dependent kinase-like 3	6.3	6.3	6.3	pKd	2
Homo sapiens	Discoidin domain-containing receptor 2	7.4	7.4	8.2	pIC50	2
Homo sapiens	Discoidin domain-containing receptor 2	8.2	6.5	8.2	pKd	6
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 5	6.7	6.7	6.7	pKd	1
Homo sapiens	Dual specificity protein kinase TTK	5.5	5.5	5.5	pKd	3
Homo sapiens	Dual-specificity tyrosine-phosphorylation regulated kinase 3	5.7	5.7	5.7	pKi	1
Homo sapiens	Dual specificty protein kinase CLK1	5.1	5.1	5.1	pKd	1
Homo sapiens	Ephrin type-A receptor 1	5.5	5.5	5.5	pKd	3
Homo sapiens	Ephrin type-A receptor 2	5.7	5.3	5.7	pKd	4
Homo sapiens	Ephrin type-A receptor 2	6.1	6.1	6.1	pKi	1
Homo sapiens	Ephrin type-A receptor 3	5.7	5.2	5.7	pKd	4
Homo sapiens	Ephrin type-A receptor 4	5.5	5.5	5.9	pKd	4
Homo sapiens	Ephrin type-A receptor 5	6.4	5.5	6.4	pKd	3
Homo sapiens	Ephrin type-A receptor 6	6.4	6.4	6.6	pKd	5
Homo sapiens	Ephrin type-A receptor 7	5.3	5.3	6.2	pKd	5
Homo sapiens	Ephrin type-A receptor 8	5.6	5.6	6	pKd	5
Homo sapiens	Ephrin type-B receptor 1	5.5	5.5	5.8	pKd	4
Homo sapiens	Ephrin type-B receptor 2	5.7	5.7	5.7	pKd	3
Homo sapiens	Ephrin type-B receptor 4	8.3	5.7	9.7	pIC50	5
Homo sapiens	Ephrin type-B receptor 4	5.8	5.4	5.8	pKd	4
Homo sapiens	Epidermal growth factor receptor erbB1	7.1	7.1	8.5	pIC50	2
Homo sapiens	Epithelial discoidin domain-containing receptor 1	8.8	8.8	8.8	pKd	4
Homo sapiens	Fibroblast growth factor receptor 1	6.2	6.2	8.3	pIC50	2
Homo sapiens	Fibroblast growth factor receptor 1	5.6	5.6	5.6	pKd	4
Homo sapiens	Fibroblast growth factor receptor 2	5.6	5.6	5.6	pKd	3
Homo sapiens	Fibroblast growth factor receptor 3	5.2	5.2	5.4	pKd	4
Homo sapiens	Fibroblast growth factor receptor 3	5.9	5.9	5.9	pKi	1
Homo sapiens	Homeodomain-interacting protein kinase 1	5.5	5.5	6	pKd	2
Homo sapiens	Homeodomain-interacting protein kinase 2	5.8	5.8	5.8	pKd	2
Homo sapiens	Homeodomain-interacting protein kinase 2	6.3	6.3	6.3	pKi	1
Homo sapiens	Homeodomain-interacting protein kinase 3	6.4	6.4	6.4	pKd	2
Homo sapiens	Homeodomain-interacting protein kinase 4	8.5	8.5	8.6	pKd	2
Homo sapiens	Homeodomain-interacting protein kinase 4	8	8	8	pKi	1
Homo sapiens	Insulin receptor	5.3	5.3	5.3	pIC50	1
Homo sapiens	Interleukin-1 receptor-associated kinase 1	5.1	5.1	5.1	pKi	1
Homo sapiens	LIM domain kinase 1	5.8	5.7	5.8	pKd	4
Homo sapiens	LIM domain kinase 1	6.2	6.2	6.2	pKi	1
Homo sapiens	LIM domain kinase 2	5	5	5	pKd	1
Homo sapiens	Macrophage colony stimulating factor receptor	7.2	7.2	7.7	pIC50	2
Homo sapiens	Macrophage colony stimulating factor receptor	7.6	7.6	7.6	pKd	3
Homo sapiens	Macrophage colony stimulating factor receptor	6.8	6.8	6.8	pKi	1
Homo sapiens	MAP kinase ERK1	7.7	7.7	7.7	pIC50	1
Homo sapiens	MAP kinase ERK2	7	7	7	pIC50	1
Homo sapiens	MAP kinase-interacting serine/threonine-protein kinase MNK1	6.6	6.6	6.6	pKd	3
Homo sapiens	MAP kinase p38 alpha	7.1	5.5	7.4	pIC50	7
Homo sapiens	MAP kinase p38 alpha	6.4	6.4	6.6	pKd	5
Homo sapiens	MAP kinase p38 alpha	7.8	7.8	7.8	pKi	1
Homo sapiens	MAP kinase p38 beta	6.6	6.6	6.7	pKd	5
Homo sapiens	MAP kinase p38 delta	5.2	5.2	5.2	pKd	2
Homo sapiens	MAP kinase p38 gamma	5.1	5	5.1	pKd	4
Homo sapiens	MAP kinase signal-integrating kinase 2	6.6	6.6	6.6	pIC50	1
Homo sapiens	MAP kinase signal-integrating kinase 2	6.9	6.6	6.9	pKd	4
Homo sapiens	MAP kinase signal-integrating kinase 2	6.5	6.5	6.5	pKi	1
Homo sapiens	Misshapen-like kinase 1	5.8	5.8	5.8	pKi	1
Homo sapiens	Mitogen-activated protein kinase 15	7.3	7.3	7.3	pKd	3
Homo sapiens	Mitogen-activated protein kinase kinase kinase 7	6.2	5.9	6.2	pKd	4
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 1	5.3	5.3	5.3	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 4	5.3	5.3	5.3	pKd	3
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 5	5.8	5.8	5.8	pKd	4
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 5	6.5	6.5	6.5	pKi	1
Homo sapiens	Mixed lineage kinase 7	8.2	8.2	8.2	pKd	3
Homo sapiens	Mixed lineage kinase 7	7.8	7.8	7.8	pKi	1
Homo sapiens	Muscle, skeletal receptor tyrosine protein kinase	6.9	6.9	6.9	pKd	3
Homo sapiens	Myosin-IIIB	5.2	5.2	5.2	pKd	1
Homo sapiens	Myosin light chain kinase	5	5	5	pKd	1
Homo sapiens	myosin light chain kinase 2	5.3	5.3	5.9	pKd	2
Homo sapiens	Nerve growth factor receptor Trk-A	5.2	5.2	5.4	pKd	4
Homo sapiens	Nerve growth factor receptor Trk-A	5.8	5.8	5.8	pKi	1
Homo sapiens	Neurotrophic tyrosine kinase receptor type 2	5.7	5.7	5.7	pKd	3
Homo sapiens	Neurotrophic tyrosine kinase receptor type 2	6.2	6.2	6.2	pKi	1
Homo sapiens	Non-receptor tyrosine-protein kinase TNK1	5.6	5.6	5.6	pKd	3
Homo sapiens	NT-3 growth factor receptor	6.2	6.2	6.2	pKd	3
Homo sapiens	NT-3 growth factor receptor	6.4	6.4	6.4	pKi	1
Homo sapiens	Platelet-derived growth factor receptor alpha	7.2	7.2	7.2	pKd	3
Homo sapiens	Platelet-derived growth factor receptor alpha	6	6	6	pKi	1
Homo sapiens	Platelet-derived growth factor receptor beta	7.4	7.2	8	pIC50	5
Homo sapiens	Platelet-derived growth factor receptor beta	7.4	7.4	7.4	pKd	5
Homo sapiens	Platelet-derived growth factor receptor beta	8.4	8.4	8.4	pKi	1
Homo sapiens	Proto-oncogene tyrosine-protein kinase MER	5.4	5.4	5.4	pKd	3
Homo sapiens	Ribosomal protein S6 kinase 1	6.4	6.4	6.4	pKi	1
Homo sapiens	Ribosomal protein S6 kinase alpha 6	5.1	5.1	5.1	pKd	6
Homo sapiens	Serine/threonine-protein kinase 10	6.8	6.8	6.9	pKd	5
Homo sapiens	Serine/threonine-protein kinase 2	6	5.8	6	pKd	4
Homo sapiens	Serine/threonine-protein kinase 2	5.8	5.8	5.8	pKi	1
Homo sapiens	Serine/threonine-protein kinase 33	5.6	5.6	5.6	pKd	3
Homo sapiens	Serine/threonine-protein kinase 36	5.4	5.3	5.4	pKd	4
Homo sapiens	Serine/threonine-protein kinase A-Raf	8.2	8.2	8.2	pIC50	1
Homo sapiens	Serine/threonine-protein kinase Aurora-A	5.4	5.4	5.4	pIC50	4
Homo sapiens	Serine/threonine-protein kinase Aurora-A	6.1	6.1	6.1	pKi	1
Homo sapiens	Serine/threonine-protein kinase Aurora-B	6.4	6.4	6.4	pKd	3
Homo sapiens	Serine/threonine-protein kinase Aurora-B	6.7	6.7	6.7	pKi	1
Homo sapiens	Serine/threonine-protein kinase Aurora-C	6.7	6.7	6.7	pKd	3
Homo sapiens	Serine/threonine-protein kinase B-raf	8.5	8.5	8.5	pEC50	1
Homo sapiens	Serine/threonine-protein kinase B-raf	7.4	5.1	9	pIC50	43
Homo sapiens	Serine/threonine-protein kinase B-raf	6.6	6.3	6.6	pKd	7
Homo sapiens	Serine/threonine-protein kinase B-raf	7.4	7.4	7.7	pKi	2
Mus musculus	Serine/threonine-protein kinase B-raf	6.9	6.9	6.9	pIC50	1
Homo sapiens	Serine/threonine protein kinase NLK	6.2	6.2	6.2	pKd	3
Homo sapiens	Serine/threonine-protein kinase PCTAIRE-2	5.8	5.8	5.8	pKd	3
Homo sapiens	Serine/threonine-protein kinase PFTAIRE-1	5.5	5.5	5.5	pKd	3
Homo sapiens	Serine/threonine-protein kinase PFTAIRE-2	5.5	5.5	5.5	pKd	2
Homo sapiens	Serine/threonine-protein kinase PLK4	5.4	5.4	5.5	pKd	4
Homo sapiens	Serine/threonine-protein kinase PLK4	6.4	6.4	6.4	pKi	1
Homo sapiens	Serine/threonine-protein kinase RAF	7.9	6.4	9	pIC50	22
Homo sapiens	Serine/threonine-protein kinase RAF	6.6	6.6	6.6	pKd	3
Homo sapiens	Serine/threonine-protein kinase RAF	8.2	8.2	8.2	pKi	1
Homo sapiens	Serine/threonine-protein kinase RIPK2	5.4	5.4	5.4	pIC50	1
Homo sapiens	Serine/threonine-protein kinase RIPK2	5.9	5.5	5.9	pKd	4
Homo sapiens	Serine/threonine-protein kinase SRPK1	5.3	5.3	5.3	pKi	1
Homo sapiens	Serine/threonine-protein kinase TAO1	5.5	5.5	6.3	pKd	2
Homo sapiens	Serine/threonine-protein kinase TAO1	6.4	6.4	6.4	pKi	1
Homo sapiens	Serine/threonine-protein kinase TAO2	6.3	6.3	6.3	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO3	5.6	5.6	5.6	pKd	2
Homo sapiens	Serine/threonine-protein kinase TNNI3K	6.6	6.6	6.6	pKd	3
Homo sapiens	SPS1/STE20-related protein kinase YSK4	7	7	7	pKd	2
Homo sapiens	Stem cell growth factor receptor	7.2	7.2	8	pIC50	4
Homo sapiens	Stem cell growth factor receptor	7.5	6.1	8	pKd	23
Homo sapiens	TGF-beta receptor type II	5.2	5.2	5.2	pKd	1
Homo sapiens	TRAF2- and NCK-interacting kinase	5.1	5.1	5.1	pKd	1
Homo sapiens	Tyrosine-protein kinase ABL	6.9	6.9	7.1	pIC50	2
Homo sapiens	Tyrosine-protein kinase ABL	6.2	5.2	6.9	pKd	40
Homo sapiens	Tyrosine-protein kinase ABL	6.8	6.8	6.8	pKi	1
Mus musculus	Tyrosine-protein kinase ABL	6.7	6.7	6.7	pIC50	1
Homo sapiens	Tyrosine-protein kinase ABL2	5.5	5.5	5.9	pKd	4
Homo sapiens	Tyrosine-protein kinase BLK	6.1	6.1	6.1	pKi	1
Homo sapiens	Tyrosine-protein kinase CSK	5.5	5.5	5.5	pKd	1
Homo sapiens	Tyrosine-protein kinase FGR	5.1	5.1	5.1	pKd	1
Homo sapiens	Tyrosine-protein kinase FRK	6.3	6.3	6.4	pKd	5
Homo sapiens	Tyrosine-protein kinase FYN	5.1	5.1	5.1	pKd	1
Homo sapiens	Tyrosine-protein kinase HCK	6.3	6.3	6.3	pIC50	2
Homo sapiens	Tyrosine-protein kinase HCK	5.1	5.1	5.1	pKd	2
Homo sapiens	Tyrosine-protein kinase JAK3	5.1	5.1	5.1	pKd	2
Homo sapiens	Tyrosine-protein kinase LCK	7.2	7.2	7.2	pIC50	1
Homo sapiens	Tyrosine-protein kinase LCK	5.6	5.2	5.6	pKd	4
Homo sapiens	Tyrosine-protein kinase Lyn	5.5	5.5	5.5	pKd	3
Homo sapiens	Tyrosine-protein kinase Lyn	6.4	6.4	6.4	pKi	1
Homo sapiens	Tyrosine-protein kinase receptor FLT3	7.5	7.2	8.7	pIC50	13
Homo sapiens	Tyrosine-protein kinase receptor FLT3	7.8	7.1	8.4	pKd	23
Homo sapiens	Tyrosine-protein kinase receptor RET	8.1	8.1	8.2	pIC50	2
Homo sapiens	Tyrosine-protein kinase receptor RET	7.9	7.4	8.1	pKd	10
Homo sapiens	Tyrosine-protein kinase receptor RET	7	7	7	pKi	1
Homo sapiens	Tyrosine-protein kinase receptor Tie-1	7.2	7.2	7.2	pKd	3
Homo sapiens	Tyrosine-protein kinase receptor UFO	5.4	5.4	5.4	pKd	3
Homo sapiens	Tyrosine-protein kinase receptor UFO	6.8	6.8	6.8	pKi	1
Homo sapiens	Tyrosine-protein kinase SRC	6.4	6.4	6.4	pIC50	1
Homo sapiens	Tyrosine-protein kinase Srms	5	5	5	pKd	3
Homo sapiens	Tyrosine-protein kinase TIE-2	8.2	8.1	9.1	pIC50	3
Homo sapiens	Tyrosine-protein kinase TIE-2	5.7	5.5	5.7	pKd	4
Homo sapiens	Vascular endothelial growth factor receptor 1	7.5	6.8	7.8	pIC50	3
Homo sapiens	Vascular endothelial growth factor receptor 1	7.5	7.5	7.5	pKd	3
Homo sapiens	Vascular endothelial growth factor receptor 1	6.5	6.5	6.5	pKi	1
Danio rerio	Vascular endothelial growth factor receptor 2	5.6	5.6	5.6	pIC50	1
Homo sapiens	Vascular endothelial growth factor receptor 2	6.3	6.3	6.3	pEC50	1
Homo sapiens	Vascular endothelial growth factor receptor 2	7.2	6	9.8	pIC50	50
Homo sapiens	Vascular endothelial growth factor receptor 2	7.2	7	7.5	pKd	6
Homo sapiens	Vascular endothelial growth factor receptor 2	7.7	7.4	10.7	pKi	4
Mus musculus	Vascular endothelial growth factor receptor 2	7.8	7.8	7.8	pIC50	1
Homo sapiens	Vascular endothelial growth factor receptor 3	7.8	7.8	8.5	pIC50	2
Homo sapiens	Vascular endothelial growth factor receptor 3	7	7	7.8	pKd	5
Homo sapiens	Vascular endothelial growth factor receptor 3	7	7	7	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 C
25

2 K
26

3 V
27

4 G
33

5 _
_

6 _
_

7 _
_

8 _
_

9 _
_

10 H
34

11 V
35

12 Y
36

13 K
37

14 Y
49

15 A
50

16 L
51

17 K
52

18 Q
53

19 I
54

20 S
62

•

αC

b.l

21 A
63

22 C
64

23 R
65

24 E
66

25 I
67

26 A
68

27 L
69

28 L
70

29 R
71

30 E
72

31 L
73

32 K
74

33 P
76

34 N
77

35 V
78

36 I
79

37 S
80

38 L
81

39 Q
82

40 K
83

••

•

hinge

linker

αD

αE

41 V
84

42 W
94

43 L
95

44 L
96

45 F
97

46 D
98

47 Y
99

48 A
100

49 E
101

50 _
_

51 H
102

52 D
103

53 L
104

54 W
105

55 H
106

56 I
107

57 I
108

58 K
109

59 F
110

60 Y
141

••

•

••

•••

•

αE

c.l

VII

VIII

61 L
142

62 H
143

63 A
144

64 N
145

65 W
146

66 V
147

67 L
148

68 H
149

69 R
150

70 D
151

71 L
152

72 K
153

73 P
154

74 A
155

75 N
156

76 I
157

77 L
158

78 V
159

79 I
171

80 A
172

•

DFG

a.l

81 D
173

82 M
174

83 G
175

84 F
176

85 A
177

••

•

••

Interaction pattern search

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