KLIFS - the structural kinase database

Structure information


PDB:	2CJM
PubMed:	17095507
Release date:	2006-04-24
Resolution:	2.3 Å

Kinase:	CDK2
Family:	CDK
Group:	CMGC
Species:	HUMAN

Quality Score:	8
Missing Residues:	0
Missing Atoms:	0

DFG conformation:	in
αC-helix conformation:	in
Salt bridge K^III.17 and E^αC.24:	Yes (3Å)


ASP rotation (xDFG.81) :	352°
PHE rotation (xDFG.82) :	18°
Activation loop position:	-3.4Å
αC-helix position:	17.2Å

G-rich loop angle:	60.4°
G-rich loop distance:	18Å
G-rich loop rotation:	69.1°

Other models from this PDB:

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

I5

H-bond protein

I6

H-bond ligand

Binding pocket sequence

Uniprot	EKIGEGTYGVVYKVALKKITAIREISLLKELNPNIVKLLDVYLVFEFLH-QDLKKFMDAFCHSHRVLHRDLKPQNLLILADFGLA
Structure:	EKIGEGTYGVVYKVALKKITAIREISLLKELNPNIVKLLDVYLVFEFLH_QDLKKFMDAFCHSHRVLHRDLKPQNLLILADFGLA

Modified residues

Residue 15 (g.l.8)

Phosphorylated tyrosine

Residue 160 (not in pocket)

Phosphorylated threonine

Orthosteric ligand

Ligand HET-code: ATP
Ligand Name: ADENOSINE-5'-TRIPHOSPHATE

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LABELS
KLIFS residue #
Amino Acid
None
COLORS
Interaction types
KLIFS (all res.)
KLIFS (interacting res.)
None
OTHER
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This ligand targets the following (sub)pockets:

Main pockets
Front
Gate
Back

Subpockets
FP-I
FP-II
BP-I-A
BP-I-B
BP-II-in
BP-II-A-in
BP-II-B-in
BP-II-out
BP-II-B
BP-III
BP-IV
BP-V

Kinase-ligand interactions

■ Hydrophobic ♦ Aromatic face-to-face ♦ Aromatic face-to-edge ▲ H-bond donor ▲ H-bond acceptor ● Ionic positive ● Ionic negative

I

g.l

II

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 T
47

■

▲

■

▲●

αC

b.l

IV

21 A
48

22 I
49

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

IV

V

GK

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

VI

c.l

VII

VIII

x

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:

Binding affinities

ChEMBL ID:CHEMBL14249
Bioaffinities: 8 records for 3 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	MAP kinase-activated protein kinase 2	5.2	4.9	5.6	pIC50	3
Homo sapiens	Mitogen-activated protein kinase kinase kinase 7	5.6	5.6	5.6	pKd	1
Homo sapiens	Tyrosine-protein kinase JAK2	5.9	5.9	5.9	pKd	4

2CJM - chain A | Cyclin-dependent kinase 2