KLIFS - the kinase structures database

Version: 3.2
Updated: 29-Oct-2025

Kinase structure
Kinase:	CDC7
Family:	CDC7
Group:	Other
Species:	HUMAN
IUPHAR/BPS ID:	1960
PDB:	4F9B
sc-PDB:
KIDFamMap:	Search
Release date:	2012-10-31
PubMed:	23064647
Chain:	A
Orthosteric ligand:	0SY

More entries for 4F9B
4F9B	Chain:	C

Structural information
DFG conformation:	in
αC-helix conformation:	in
G-rich loop angle (distance):	47.6° (15Å)
G-rich loop rotation:	42.7°
Quality Score:	7.4
Resolution:	2.5 Å
Missing Residues:	0
Missing Atoms:	0

Ligand binding mode
Pockets	Subpockets	Waters
front		Cluster I4 I5	Ligand No No	Protein Yes No

Pocket alignment
Uniprot sequence:	DKIGEGTFSSVYLIALKHLRIAAELQCLTVAGDNVMGVKYCVIAMPYLE-HESFLD--IRIHQFGIVHRDVKPSNFLYLVDFGLA
Sequence structure:	DKIGEGTFSSVYLIALKHLRIAAELQCLTVAGDNVMGVKYCVIAMPYLE_HESFLD__IRIHQFGIVHRDVKPSNFLYLVDFGLA

Ligand affinity
ChEMBL ID:	CHEMBL225519
Bioaffinities:	92 records for 70 kinases

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Activin receptor type-1	6	6	6	pKi	1
Homo sapiens	BR serine/threonine-protein kinase 1	6	6	6	pKi	1
Homo sapiens	cAMP-dependent protein kinase alpha-catalytic subunit	5.7	5.7	5.7	pKi	1
Homo sapiens	Casein kinase I alpha	7.5	7.5	7.5	pKi	1
Homo sapiens	Casein kinase I delta	7.3	7.3	7.3	pKi	1
Homo sapiens	Casein kinase I gamma 1	6.6	6.6	6.6	pKi	1
Homo sapiens	Casein kinase I gamma 2	7.2	7.2	7.2	pKi	1
Homo sapiens	Casein kinase II alpha	5.5	5.5	5.5	pKi	1
Homo sapiens	Casein kinase I isoform gamma-3	6.8	6.8	6.8	pKi	1
Homo sapiens	Cell division cycle 7-related protein kinase	8	8	8	pIC50	4
Homo sapiens	Cell division cycle 7-related protein kinase	8.6	8.6	8.6	pKi	1
Homo sapiens	Cell division protein kinase 8	8	8	8	pKi	1
Homo sapiens	cGMP-dependent protein kinase 1 beta	7.7	7.7	7.7	pKi	1
Homo sapiens	cGMP-dependent protein kinase 2	7.1	7.1	7.1	pKi	1
Homo sapiens	Cyclin-dependent kinase 1	6.6	6.6	6.8	pIC50	2
Homo sapiens	Cyclin-dependent kinase 1	6.2	6.2	6.2	pKi	1
Homo sapiens	Cyclin-dependent kinase 2	6.6	6.6	6.6	pIC50	1
Homo sapiens	Cyclin-dependent kinase 2	6.5	6.5	6.5	pKi	1
Homo sapiens	Cyclin-dependent kinase 5	6.3	6.3	6.3	pIC50	1
Homo sapiens	Cyclin-dependent kinase 5	6.7	6.7	6.7	pKi	1
Homo sapiens	Cyclin-dependent kinase 9	7.5	7.5	7.5	pIC50	2
Homo sapiens	Cyclin-dependent kinase 9	8	8	8	pKi	1
Homo sapiens	Death-associated protein kinase 3	7.2	7.2	7.2	pKi	1
Homo sapiens	Dual specificity protein kinase CLK2	6.6	6.6	6.6	pKi	1
Homo sapiens	Dual specificity protein kinase CLK4	8.4	8.4	8.4	pKi	1
Homo sapiens	Dual-specificity tyrosine-phosphorylation regulated kinase 1A	7.7	7.7	7.7	pKi	1
Homo sapiens	Dual specificity tyrosine-phosphorylation-regulated kinase 1B	8	8	8	pKi	1
Homo sapiens	Dual-specificity tyrosine-phosphorylation regulated kinase 3	7.3	7.3	7.3	pKi	1
Homo sapiens	Dual specificity tyrosine-phosphorylation-regulated kinase 4	6.7	6.7	6.7	pKi	1
Homo sapiens	Glycogen synthase kinase-3 alpha	7.2	7.2	7.2	pKi	1
Homo sapiens	Glycogen synthase kinase-3 beta	6.7	6.7	6.7	pIC50	1
Homo sapiens	Glycogen synthase kinase-3 beta	7.4	7.4	7.4	pKi	1
Homo sapiens	Homeodomain-interacting protein kinase 2	6.7	6.7	6.7	pKi	1
Homo sapiens	Homeodomain-interacting protein kinase 4	6.2	6.2	6.2	pKi	1
Homo sapiens	Interleukin-1 receptor-associated kinase 1	7.1	7.1	7.1	pKi	1
Homo sapiens	Interleukin-1 receptor-associated kinase 4	5.1	5.1	5.1	pKi	1
Homo sapiens	Leucine-rich repeat serine/threonine-protein kinase 2	6.1	6.1	6.1	pKi	1
Homo sapiens	MAP kinase-activated protein kinase 2	6.3	6.3	6.8	pIC50	2
Homo sapiens	MAP kinase-activated protein kinase 2	6.1	6.1	6.1	pKi	1
Homo sapiens	MAP kinase-activated protein kinase 3	4.2	4.2	4.2	pIC50	1
Homo sapiens	MAP kinase-activated protein kinase 5	6.3	6.3	6.3	pIC50	1
Homo sapiens	MAP kinase ERK2	5.6	5.6	5.6	pKi	1
Homo sapiens	MAP kinase-interacting serine/threonine-protein kinase MNK1	5.6	5.6	5.6	pIC50	2
Homo sapiens	MAP kinase p38 delta	7.1	7.1	7.1	pKi	1
Homo sapiens	MAP kinase p38 gamma	7.5	7.5	7.5	pKi	1
Homo sapiens	MAP kinase signal-integrating kinase 2	6.8	6.8	6.8	pIC50	1
Homo sapiens	MAP kinase signal-integrating kinase 2	6.4	6.4	6.4	pKi	1
Homo sapiens	MAP/microtubule affinity-regulating kinase 2	5.5	5.5	5.5	pKi	1
Homo sapiens	Misshapen-like kinase 1	6.3	6.3	6.3	pKi	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 2	5.9	5.9	5.9	pKi	1
Homo sapiens	PAS domain-containing serine/threonine-protein kinase	6.6	6.6	6.6	pKi	1
Homo sapiens	PDZ-binding kinase	6.3	6.3	6.3	pKi	1
Homo sapiens	Protein kinase C delta	6.2	6.2	6.2	pKi	1
Homo sapiens	Protein kinase C nu	6.1	6.1	6.1	pKi	1
Homo sapiens	Protein kinase C theta	7.4	7.4	7.4	pKi	1
Homo sapiens	Protein kinase C zeta	5.7	5.7	5.7	pKi	1
Homo sapiens	Protein kinase N2	8.3	8.3	8.3	pKi	1
Homo sapiens	Rho-associated protein kinase 1	7	7	7	pKi	1
Homo sapiens	Rho-associated protein kinase 2	7.3	7.3	7.3	pKi	1
Homo sapiens	Ribosomal protein S6 kinase 1	5.7	5.7	5.7	pKi	1
Homo sapiens	Ribosomal protein S6 kinase alpha 3	5.7	5.7	5.7	pKi	2
Homo sapiens	Ribosomal protein S6 kinase alpha 4	5.5	5.5	5.5	pIC50	2
Homo sapiens	Ribosomal protein S6 kinase alpha 5	5.6	5.6	5.6	pIC50	2
Homo sapiens	Ribosomal protein S6 kinase alpha 5	6	6	6	pKi	2
Homo sapiens	Serine/threonine-protein kinase 17A	7.2	7.2	7.2	pKi	1
Homo sapiens	Serine/threonine-protein kinase 2	5.2	5.2	5.2	pKi	1
Homo sapiens	Serine/threonine-protein kinase AKT	5.3	5.3	5.3	pKi	1
Homo sapiens	Serine/threonine-protein kinase Chk2	6	6	6	pIC50	1
Homo sapiens	Serine/threonine-protein kinase D2	6.2	6.2	6.2	pKi	1
Homo sapiens	Serine/threonine-protein kinase MRCK-A	5.3	5.3	5.3	pKi	1
Homo sapiens	Serine/threonine-protein kinase Nek4	5.9	5.9	5.9	pKi	1
Homo sapiens	Serine/threonine-protein kinase PIM3	5.8	5.8	5.8	pKi	1
Homo sapiens	Serine/threonine-protein kinase PLK1	6	6	6	pIC50	1
Homo sapiens	Serine/threonine-protein kinase PLK1	5.5	5.5	5.5	pKi	1
Homo sapiens	Serine/threonine-protein kinase PLK3	6.3	6.3	6.3	pKi	1
Homo sapiens	Serine/threonine-protein kinase PLK4	6.1	6.1	6.1	pKi	1
Homo sapiens	Serine/threonine-protein kinase PRKX	6.2	6.2	6.2	pKi	1
Homo sapiens	Serine/threonine-protein kinase Sgk2	5.3	5.3	5.3	pKi	1
Homo sapiens	Serine/threonine-protein kinase TAO1	5.6	5.6	5.6	pKi	1
Homo sapiens	Tyrosine-protein kinase JAK3	5.6	5.6	5.6	pKi	2

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 D
62

2 K
63

3 I
64

4 G
65

5 E
66

6 G
67

7 T
68

8 F
69

9 S
70

10 S
71

11 V
72

12 Y
73

13 L
74

14 I
87

15 A
88

16 L
89

17 K
90

18 H
91

19 L
92

20 R
100

•

••

αC

b.l

21 I
101

22 A
102

23 A
103

24 E
104

25 L
105

26 Q
106

27 C
107

28 L
108

29 T
109

30 V
110

31 A
111

32 G
112

33 D
115

34 N
116

35 V
117

36 M
118

37 G
119

38 V
120

39 K
121

40 Y
122

•

hinge

linker

αD

αE

41 C
123

42 V
131

43 I
132

44 A
133

45 M
134

46 P
135

47 Y
136

48 L
137

49 E
138

50 _
_

51 H
139

52 E
140

53 S
141

54 F
142

55 L
143

56 D
144

57 _
_

58 _
_

59 I
145

60 R
167

•

••

αE

c.l

VII

VIII

61 I
168

62 H
169

63 Q
170

64 F
171

65 G
172

66 I
173

67 V
174

68 H
175

69 R
176

70 D
177

71 V
178

72 K
179

73 P
180

74 S
181

75 N
182

76 F
183

77 L
184

78 Y
185

79 L
194

80 V
195

•

DFG

a.l

81 D
196

82 F
197

83 G
198

84 L
199

85 A
200

Interaction pattern search

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