KLIFS - the kinase structures database

Version: 3.2
Updated: 29-Oct-2025

Kinase structure
Kinase:	CDK9
Family:	CDK
Group:	CMGC
Species:	HUMAN
IUPHAR/BPS ID:	1981
PDB:	3BLR
sc-PDB:
KIDFamMap:	Search
Release date:	2008-07-01
PubMed:	18566585
Chain:	A
Orthosteric ligand:	CPB

Structural information
DFG conformation:	in
αC-helix conformation:	in
G-rich loop angle (distance):	50.8° (16.2Å)
G-rich loop rotation:	47.7°
Quality Score:	8
Resolution:	2.8 Å
Missing Residues:	0
Missing Atoms:	0

Ligand binding mode
Pockets	Subpockets
front	FP-I

Pocket alignment
Uniprot sequence:	AKIGQGTFGEVFKVALKKVTALREIKILQLLKENVVNLIEIYLVFDFCE-HDLAGLLSNYIHRNKILHRDMKAANVLILADFGLA
Sequence structure:	AKIGQGTFGEVFKVALKKVTALREIKILQLLKENVVNLIEIYLVFDFCE_HDLAGLLSNYIHRNKILHRDMKAANVLILADFGLA

Ligand affinity
ChEMBL ID:	CHEMBL428690
Bioaffinities:	318 records for 144 kinases

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Activin receptor type-1	5.7	5.7	5.7	pKd	2
Homo sapiens	Activin receptor type-2A	5.5	5.5	5.5	pKd	1
Homo sapiens	Activin receptor type-2B	5.6	5.6	5.6	pKd	2
Homo sapiens	Adaptor-associated kinase	5.3	5.3	5.3	pKd	2
Homo sapiens	ALK tyrosine kinase receptor	6.2	6.2	6.2	pKd	2
Homo sapiens	AMP-activated protein kinase, alpha-1 subunit	5.2	5.2	5.2	pKd	1
Homo sapiens	Bone morphogenetic protein receptor type-1B	6.4	6.4	6.4	pKd	1
Homo sapiens	CaM kinase II alpha	5.8	5.8	5.9	pKd	3
Homo sapiens	CaM kinase II beta	5.3	5.3	5.6	pKd	2
Homo sapiens	CaM kinase II delta	5.8	5.8	5.8	pKd	1
Homo sapiens	CaM kinase II gamma	5.6	5.6	5.6	pKd	1
Homo sapiens	CaM kinase IV	5.5	5.5	5.5	pKd	2
Homo sapiens	CaM-kinase kinase alpha	7.1	7.1	7.7	pKd	3
Homo sapiens	CaM-kinase kinase beta	6.4	6.4	6.5	pKd	3
Homo sapiens	Casein kinase I alpha	5.5	5.5	5.5	pKd	1
Homo sapiens	Casein kinase I gamma 1	5.9	5.9	5.9	pKd	1
Homo sapiens	Casein kinase I isoform alpha-like	5.6	5.6	5.6	pKd	1
Plasmodium falciparum (isolate 3D7)	Cell division control protein 2 homolog	5.5	5.5	5.5	pKd	1
Homo sapiens	Cell division cycle 2-like protein kinase 6	7.2	7.2	7.2	pKd	2
Homo sapiens	Cell division protein kinase 8	6.9	6.9	6.9	pKd	2
Homo sapiens	Citron Rho-interacting kinase	7	7	7	pKd	2
Homo sapiens	c-Jun N-terminal kinase 1	5.8	5.8	5.8	pKd	1
Homo sapiens	c-Jun N-terminal kinase 3	5.3	5.3	5.3	pKd	2
Homo sapiens	Cyclin-dependent kinase 1	7.5	7.5	7.5	pIC50	4
Homo sapiens	Cyclin-dependent kinase 1	7.2	7.2	7.2	pKi	1
Homo sapiens	Cyclin-dependent kinase 2	6.8	6.8	7.4	pIC50	4
Homo sapiens	Cyclin-dependent kinase 2	6.3	6.3	6.7	pKd	3
Homo sapiens	Cyclin-dependent kinase 2	6.7	6.7	6.7	pKi	1
Homo sapiens	Cyclin-dependent kinase 3	6.4	6.4	6.4	pKd	2
Homo sapiens	Cyclin-dependent kinase 4	7	7	7	pIC50	3
Homo sapiens	Cyclin-dependent kinase 4	8.1	8.1	8.5	pKd	2
Homo sapiens	Cyclin-dependent kinase 5	7	7	7.4	pKd	3
Homo sapiens	Cyclin-dependent kinase 6	7.1	7.1	7.1	pIC50	2
Homo sapiens	Cyclin-dependent kinase 7	6.1	6.1	6.1	pIC50	1
Homo sapiens	Cyclin-dependent kinase 7	7.6	7.6	7.6	pKd	2
Homo sapiens	Cyclin-dependent kinase 9	7.7	7.7	7.7	pIC50	2
Homo sapiens	Cyclin-dependent kinase 9	8.2	8.2	8.2	pKd	2
Homo sapiens	Cyclin-dependent kinase 9	8.5	8.5	8.5	pKi	1
Homo sapiens	Cyclin-dependent kinase-like 5	8.2	8.2	8.2	pKd	1
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 3	5.9	5.9	5.9	pKd	1
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 4	5.6	5.6	5.6	pKd	1
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 5	6.8	6.8	6.8	pKd	1
Mus musculus	Dual specificity protein kinase CLK1	5.9	5.9	5.9	pIC50	1
Homo sapiens	Dual specificity protein kinase CLK2	5.7	5.7	5.9	pKd	3
Homo sapiens	Dual specificity protein kinase CLK3	5.8	5.8	6	pKd	3
Rattus norvegicus	Dual specificity tyrosine-phosphorylation-regulated kinase 1A	6.5	6.5	6.5	pIC50	1
Homo sapiens	Dual-specificity tyrosine-phosphorylation regulated kinase 1A	7.1	7.1	7.1	pKd	1
Homo sapiens	Dual specificity tyrosine-phosphorylation-regulated kinase 1B	7.1	7.1	7.1	pKd	2
Homo sapiens	Dual specificty protein kinase CLK1	5.8	5.7	5.8	pKd	3
Homo sapiens	Ephrin type-A receptor 1	5.6	5.6	5.6	pKd	1
Homo sapiens	Ephrin type-A receptor 2	5.6	5.6	5.6	pKd	2
Homo sapiens	Ephrin type-A receptor 3	5.5	5.5	5.5	pKd	2
Homo sapiens	Ephrin type-A receptor 5	5.4	5.4	5.5	pKd	2
Homo sapiens	Ephrin type-B receptor 1	5.7	5.7	5.8	pKd	2
Homo sapiens	Epidermal growth factor receptor erbB1	4.7	4.7	5.1	pIC50	2
Homo sapiens	Epidermal growth factor receptor erbB1	5.8	5.4	6.3	pKd	14
Homo sapiens	Eukaryotic translation initiation factor 2-alpha kinase 1	6.1	6.1	6.1	pKd	1
Homo sapiens	Glycogen synthase kinase-3 alpha	5.9	5.9	5.9	pKd	2
Homo sapiens	Glycogen synthase kinase-3 beta	6.1	6.1	6.1	pKd	2
Homo sapiens	G protein-coupled receptor kinase 7	6	6	6	pKd	1
Homo sapiens	Homeodomain-interacting protein kinase 1	5.2	5.2	5.2	pKd	1
Homo sapiens	Homeodomain-interacting protein kinase 2	5.4	5.4	5.4	pKd	1
Homo sapiens	Homeodomain-interacting protein kinase 3	5.4	5.4	5.4	pKd	1
Homo sapiens	Homeodomain-interacting protein kinase 4	5.7	5.7	5.7	pKd	1
Homo sapiens	Inhibitor of nuclear factor kappa B kinase epsilon subunit	5.5	5.5	5.5	pKd	2
Homo sapiens	Interferon-induced, double-stranded RNA-activated protein kinase	5.3	5.3	5.3	pKd	2
Homo sapiens	Interleukin-1 receptor-associated kinase 1	6.3	6.3	6.3	pKd	1
Homo sapiens	Interleukin-1 receptor-associated kinase 4	5.8	5.8	5.8	pKd	1
Homo sapiens	Leucine-rich repeat serine/threonine-protein kinase 2	5.7	5.7	6	pKd	2
Homo sapiens	Leukocyte tyrosine kinase receptor	5.7	5.7	5.7	pKd	2
Homo sapiens	Macrophage colony stimulating factor receptor	5.6	5.6	5.6	pKd	2
Homo sapiens	MAP kinase signal-integrating kinase 2	5.5	5.5	5.7	pKd	3
Homo sapiens	Misshapen-like kinase 1	5.9	5.9	5.9	pKd	1
Homo sapiens	Mitogen-activated protein kinase 15	6.5	6.5	6.5	pKd	2
Homo sapiens	Mitogen-activated protein kinase 7	6.2	6.2	6.2	pKd	2
Homo sapiens	Mitogen-activated protein kinase kinase kinase 10	5.3	5.3	5.3	pKd	2
Homo sapiens	Mitogen-activated protein kinase kinase kinase 2	5.2	5.2	5.2	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 3	5	5	5	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 7	5.5	5.5	5.5	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 9	5.2	5.2	5.2	pKd	2
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 1	5.5	5.5	5.5	pKd	2
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 2	7.1	7.1	7.1	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 3	5.4	5.4	5.4	pKd	2
Homo sapiens	Myotonin-protein kinase	6.2	6.2	6.2	pKd	2
Homo sapiens	NUAK family SNF1-like kinase 2	5.9	5.9	5.9	pKd	2
Homo sapiens	Phosphorylase kinase gamma subunit 1	5.7	5.7	5.7	pKd	2
Homo sapiens	Phosphorylase kinase gamma subunit 2	5.5	5.5	5.7	pKd	3
Homo sapiens	Platelet-derived growth factor receptor alpha	5.2	5.2	5.2	pKd	1
Homo sapiens	Protein kinase C alpha	5.6	5.6	5.6	pIC50	1
Homo sapiens	Protein kinase C delta	6.1	6.1	6.1	pIC50	1
Homo sapiens	Protein kinase C delta	6.2	6.2	6.2	pKd	2
Homo sapiens	Protein kinase C epsilon	6.3	6.3	6.3	pIC50	1
Homo sapiens	Protein kinase C epsilon	6.4	6.4	6.4	pKd	2
Homo sapiens	Protein kinase C eta	6.5	6.5	6.5	pKd	2
Homo sapiens	Protein kinase C mu	6.3	6.3	6.3	pKd	2
Homo sapiens	Protein kinase C nu	6.8	6.8	6.8	pKd	2
Homo sapiens	Protein kinase C theta	6.5	6.5	6.5	pKd	2
Homo sapiens	Protein kinase N1	5.5	5.5	5.5	pKd	2
Homo sapiens	Protein tyrosine kinase 2 beta	5.5	5.5	5.5	pKd	1
Homo sapiens	Proto-oncogene tyrosine-protein kinase MER	5.2	5.2	5.2	pKd	2
Homo sapiens	Receptor protein-tyrosine kinase erbB-2	4.8	4.8	4.8	pIC50	1
Homo sapiens	Receptor protein-tyrosine kinase erbB-4	5.3	5.3	5.3	pKd	1
Homo sapiens	Receptor tyrosine-protein kinase erbB-3	5	5	5	pKd	1
Homo sapiens	Rho-associated protein kinase 1	5.9	5.9	5.9	pKd	1
Homo sapiens	Rho-associated protein kinase 2	5.8	5.8	5.8	pKd	1
Homo sapiens	Rhodopsin kinase	6.2	6.2	6.2	pKd	1
Homo sapiens	Ribosomal protein S6 kinase 1	5.4	5.4	5.4	pKd	1
Homo sapiens	Ribosomal protein S6 kinase alpha 1	5.6	5.6	6.1	pKd	8
Homo sapiens	Ribosomal protein S6 kinase alpha 2	5.8	5.4	5.8	pKd	8
Homo sapiens	Ribosomal protein S6 kinase alpha 3	6	6	6	pKd	2
Homo sapiens	Ribosomal protein S6 kinase alpha 4	5.9	5.9	5.9	pKd	4
Homo sapiens	Ribosomal protein S6 kinase alpha 5	5.7	5.7	5.7	pKd	2
Homo sapiens	Ribosomal protein S6 kinase alpha 6	6.1	5.7	6.1	pKd	6
Homo sapiens	Serine/threonine-protein kinase 17A	5.4	5.4	5.4	pKd	1
Homo sapiens	Serine/threonine-protein kinase 17B	5.7	5.3	5.7	pKd	3
Homo sapiens	Serine/threonine-protein kinase 32A	5.3	5.3	5.3	pKd	1
Homo sapiens	Serine/threonine-protein kinase 33	5.8	5.8	5.8	pKd	2
Homo sapiens	Serine/threonine-protein kinase 35	6.4	6.4	6.4	pKd	1
Homo sapiens	Serine/threonine-protein kinase D2	6	6	6	pKd	2
Homo sapiens	Serine/threonine-protein kinase DCLK1	5.7	5.7	5.7	pKd	2
Homo sapiens	Serine/threonine-protein kinase DCLK3	6	6	6	pKd	2
Homo sapiens	Serine/threonine-protein kinase GAK	6.4	6	6.4	pKd	3
Homo sapiens	Serine/threonine-protein kinase ICK	9.2	9.2	9.2	pKd	1
Homo sapiens	Serine/threonine-protein kinase MAK	7.6	7.6	7.6	pKd	1
Homo sapiens	Serine/threonine-protein kinase MRCK-A	5	5	5	pKd	2
Homo sapiens	Serine/threonine-protein kinase MRCK beta	5.5	5.5	5.5	pKd	2
Homo sapiens	Serine/threonine-protein kinase MST2	5	5	5	pKd	2
Homo sapiens	Serine/threonine-protein kinase PCTAIRE-1	6.4	6.4	6.8	pKd	3
Homo sapiens	Serine/threonine-protein kinase PCTAIRE-2	6.3	6.3	6.3	pKd	2
Homo sapiens	Serine/threonine-protein kinase PCTAIRE-3	6	6	6	pKd	2
Homo sapiens	Serine/threonine-protein kinase PFTAIRE-1	7	7	7	pKd	2
Homo sapiens	Serine/threonine-protein kinase PFTAIRE-2	6.5	6.5	6.5	pKd	1
Homo sapiens	Serine/threonine-protein kinase PIM1	6.3	6.3	6.3	pKd	3
Homo sapiens	Serine/threonine-protein kinase PIM2	6.1	6.1	6.2	pKd	3
Homo sapiens	Serine/threonine-protein kinase PIM3	6.2	6.2	6.2	pKd	2
Homo sapiens	Serine/threonine-protein kinase PLK4	5.1	5.1	5.5	pKd	2
Homo sapiens	Serine/threonine-protein kinase receptor R3	5.4	5.4	5.4	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO1	6.9	6.9	6.9	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO2	6.6	6.6	6.6	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO3	7	7	7	pKd	1
Homo sapiens	Serine/threonine-protein kinase TBK1	6.3	6.3	6.3	pKd	1
Homo sapiens	Serine/threonine-protein kinase TNNI3K	7.3	7.3	7.3	pKd	2
Homo sapiens	Serine/threonine-protein kinase ULK2	6.3	6.3	6.3	pKd	1
Homo sapiens	Stem cell growth factor receptor	5.3	5.1	5.3	pKd	5
Homo sapiens	TGF-beta receptor type II	5.3	5.3	5.3	pKd	2
Homo sapiens	Tyrosine-protein kinase ABL	5.8	5.2	6.1	pKd	12
Homo sapiens	Tyrosine-protein kinase FRK	5.9	5.9	5.9	pKd	1
Homo sapiens	Tyrosine-protein kinase JAK2	5.3	5.3	5.3	pKd	2
Homo sapiens	Tyrosine-protein kinase JAK3	5.8	5.8	5.8	pKd	2
Homo sapiens	Tyrosine-protein kinase LCK	5	5	5	pIC50	1
Homo sapiens	Tyrosine-protein kinase receptor FLT3	5.3	5.2	5.5	pKd	8
Homo sapiens	Tyrosine-protein kinase receptor UFO	5.5	5.5	5.5	pKd	2
Homo sapiens	Tyrosine-protein kinase Srms	5.9	5.9	5.9	pKd	2
Homo sapiens	Tyrosine-protein kinase TYK2	6.8	6.8	7.5	pKd	4

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 A
23

2 K
24

3 I
25

4 G
26

5 Q
27

6 G
28

7 T
29

8 F
30

9 G
31

10 E
32

11 V
33

12 F
34

13 K
35

14 V
45

15 A
46

16 L
47

17 K
48

18 K
49

19 V
50

20 T
62

•

αC

b.l

21 A
63

22 L
64

23 R
65

24 E
66

25 I
67

26 K
68

27 I
69

28 L
70

29 Q
71

30 L
72

31 L
73

32 K
74

33 E
76

34 N
77

35 V
78

36 V
79

37 N
80

38 L
81

39 I
82

40 E
83

•

hinge

linker

αD

αE

41 I
84

42 Y
100

43 L
101

44 V
102

45 F
103

46 D
104

47 F
105

48 C
106

49 E
107

50 _
_

51 H
108

52 D
109

53 L
110

54 A
111

55 G
112

56 L
113

57 L
114

58 S
115

59 N
116

60 Y
139

••

•

••

•

αE

c.l

VII

VIII

61 I
140

62 H
141

63 R
142

64 N
143

65 K
144

66 I
145

67 L
146

68 H
147

69 R
148

70 D
149

71 M
150

72 K
151

73 A
152

74 A
153

75 N
154

76 V
155

77 L
156

78 I
157

79 L
165

80 A
166

•

DFG

a.l

81 D
167

82 F
168

83 G
169

84 L
170

85 A
171

•

Interaction pattern search

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