KLIFS - the kinase structures database

Version: 3.2
Updated: 29-Oct-2025

Kinase structure
Kinase:	CDK2
Family:	CDK
Group:	CMGC
Species:	HUMAN
IUPHAR/BPS ID:	1973
PDB:	2FVD
sc-PDB:
KIDFamMap:	Search
Release date:	2006-10-10
PubMed:	17064073
Chain:	A
Orthosteric ligand:	LIA

Structural information
DFG conformation:	in
αC-helix conformation:	out
G-rich loop angle (distance):	51.7° (15.2Å)
G-rich loop rotation:	52.2°
Quality Score:	8.2
Resolution:	1.85 Å
Missing Residues:	3
Missing Atoms:	6

Ligand binding mode
Pockets	Subpockets	Waters
front	FP-I	Cluster I2 I4 I5 I9	Ligand No No Yes Yes	Protein Yes No Yes No

Pocket alignment
Uniprot sequence:	EKIGEGTYGVVYKVALKKITAIREISLLKELNPNIVKLLDVYLVFEFLH-QDLKKFMDAFCHSHRVLHRDLKPQNLLILADFGLA
Sequence structure:	EKIGEGTYGVVYKVALKKI___REISLLKELNPNIVKLLDVYLVFEFLH_QDLKKFMDAFCHSHRVLHRDLKPQNLLILADFGLA

Ligand affinity
ChEMBL ID:	CHEMBL384304
Bioaffinities:	61 records for 50 kinases

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	CaM kinase II alpha	5.7	5.7	5.7	pKd	1
Homo sapiens	CaM kinase II beta	6.1	6.1	6.1	pKd	1
Homo sapiens	CaM kinase II delta	5.9	5.9	5.9	pKd	1
Homo sapiens	CaM kinase II gamma	5.7	5.7	5.7	pKd	1
Homo sapiens	CaM-kinase kinase beta	5.9	5.9	5.9	pKd	1
Plasmodium falciparum (isolate 3D7)	Cell division control protein 2 homolog	6.2	6.2	6.2	pKd	1
Homo sapiens	Cyclin-dependent kinase 1	8.7	8.7	8.7	pKi	1
Homo sapiens	Cyclin-dependent kinase 2	9.3	9.3	9.3	pKd	1
Homo sapiens	Cyclin-dependent kinase 2	8.5	8.5	8.5	pKi	1
Homo sapiens	Cyclin-dependent kinase 3	8.5	8.5	8.5	pKd	1
Homo sapiens	Cyclin-dependent kinase 4	9.1	9.1	9.2	pKd	2
Homo sapiens	Cyclin-dependent kinase 5	8.1	8.1	8.1	pKd	1
Homo sapiens	Cyclin-dependent kinase 7	9.2	9.2	9.2	pKd	1
Homo sapiens	Cyclin-dependent kinase 9	7.8	7.8	7.8	pKd	1
Homo sapiens	Cyclin-dependent kinase-like 5	5.4	5.4	5.4	pKd	1
Homo sapiens	Dual specificity protein kinase CLK2	7.1	7.1	7.1	pKd	1
Homo sapiens	Dual specificity protein kinase CLK3	7.9	7.9	7.9	pKd	1
Homo sapiens	Dual specificity protein kinase CLK4	6.5	6.5	6.5	pKd	1
Homo sapiens	Dual specificity protein kinase TTK	5.2	5.2	5.2	pKd	1
Homo sapiens	Dual-specificity tyrosine-phosphorylation regulated kinase 1A	7.6	7.6	7.6	pKd	1
Homo sapiens	Dual specificity tyrosine-phosphorylation-regulated kinase 1B	6.6	6.6	6.6	pKd	1
Homo sapiens	Dual specificty protein kinase CLK1	7.2	7.2	7.2	pKd	1
Homo sapiens	Epidermal growth factor receptor erbB1	5.2	5	5.3	pKd	8
Homo sapiens	Glycogen synthase kinase-3 alpha	6.6	6.6	6.6	pKd	1
Homo sapiens	Glycogen synthase kinase-3 beta	6.6	6.6	6.6	pKd	1
Homo sapiens	Glycogen synthase kinase-3 beta	5.1	5.1	5.1	pKi	1
Homo sapiens	Mitogen-activated protein kinase 15	7.2	7.2	7.2	pKd	1
Homo sapiens	Mitogen-activated protein kinase 7	7	7	7	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 1	5.5	5.5	5.5	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 2	5.5	5.5	5.5	pKd	1
Homo sapiens	Myotonin-protein kinase	6.2	6.2	6.2	pKd	1
Homo sapiens	PITSLRE serine/threonine-protein kinase CDC2L1	5.6	5.6	5.6	pKd	1
Homo sapiens	PITSLRE serine/threonine-protein kinase CDC2L2	5.5	5.5	5.5	pKd	1
Homo sapiens	Protein kinase N2	5.1	5.1	5.1	pKd	1
Homo sapiens	Rho-associated protein kinase 1	5.7	5.7	5.7	pKd	1
Homo sapiens	Rho-associated protein kinase 2	6.1	6.1	6.1	pKd	1
Homo sapiens	Ribosomal protein S6 kinase alpha 2	6.4	6.4	6.4	pKd	2
Homo sapiens	Serine/threonine-protein kinase 10	6.4	6.4	6.4	pKd	1
Homo sapiens	Serine/threonine-protein kinase 2	7	7	7	pKd	1
Homo sapiens	Serine/threonine-protein kinase DCLK3	6.2	6.2	6.2	pKd	1
Homo sapiens	Serine/threonine-protein kinase ICK	8.7	8.7	8.7	pKd	1
Homo sapiens	Serine/threonine-protein kinase MAK	8	8	8	pKd	1
Homo sapiens	Serine/threonine-protein kinase PCTAIRE-1	9.3	9.3	9.3	pKd	1
Homo sapiens	Serine/threonine-protein kinase PCTAIRE-2	9.1	9.1	9.1	pKd	1
Homo sapiens	Serine/threonine-protein kinase PCTAIRE-3	7.7	7.7	7.7	pKd	1
Homo sapiens	Serine/threonine-protein kinase PFTAIRE-1	8	8	8	pKd	1
Homo sapiens	Serine/threonine-protein kinase PFTAIRE-2	8.1	8.1	8.1	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO1	6.2	6.2	6.2	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO2	6.1	6.1	6.1	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO3	6.7	6.7	6.7	pKd	1
Homo sapiens	Serine/threonine-protein kinase TNNI3K	5.4	5.4	5.4	pKd	1
Homo sapiens	Tyrosine-protein kinase ABL	5.6	5.6	5.6	pKd	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 E
8

2 K
9

3 I
10

4 G
11

5 E
12

6 G
13

7 T
14

8 Y
15

9 G
16

10 V
17

11 V
18

12 Y
19

13 K
20

14 V
30

15 A
31

16 L
32

17 K
33

18 K
34

19 I
35

20 _
_

•

αC

b.l

21 _
_

22 _
_

23 R
50

24 E
51

25 I
52

26 S
53

27 L
54

28 L
55

29 K
56

30 E
57

31 L
58

32 N
59

33 P
61

34 N
62

35 I
63

36 V
64

37 K
65

38 L
66

39 L
67

40 D
68

hinge

linker

αD

αE

41 V
69

42 Y
77

43 L
78

44 V
79

45 F
80

46 E
81

47 F
82

48 L
83

49 H
84

50 _
_

51 Q
85

52 D
86

53 L
87

54 K
88

55 K
89

56 F
90

57 M
91

58 D
92

59 A
93

60 F
117

•

••

•

αE

c.l

VII

VIII

61 C
118

62 H
119

63 S
120

64 H
121

65 R
122

66 V
123

67 L
124

68 H
125

69 R
126

70 D
127

71 L
128

72 K
129

73 P
130

74 Q
131

75 N
132

76 L
133

77 L
134

78 I
135

79 L
143

80 A
144

•

DFG

a.l

81 D
145

82 F
146

83 G
147

84 L
148

85 A
149

•

Interaction pattern search

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