2CJM - chain A | Cyclin-dependent kinase 2
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 KIII.17 and EαC.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

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I5
H-bond protein
I6
H-bond ligand
Binding pocket sequence
UniprotEKIGEGTYGVVYKVALKKITAIREISLLKELNPNIVKLLDVYLVFEFLH-QDLKKFMDAFCHSHRVLHRDLKPQNLLILADFGLA
Structure:EKIGEGTYGVVYKVALKKITAIREISLLKELNPNIVKLLDVYLVFEFLH_QDLKKFMDAFCHSHRVLHRDLKPQNLLILADFGLA


Modified residues
Residue 15 (g.l.8)
Phosphorylated tyrosine
Residue 160 (not in pocket)
Phosphorylated threonine
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: ATP
Ligand Name: ADENOSINE-5'-TRIPHOSPHATE

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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
Kinase-ligand interaction pattern
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

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

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensMAP kinase-activated protein kinase 25.24.95.6pIC503
Homo sapiensMitogen-activated protein kinase kinase kinase 75.65.65.6pKd1
Homo sapiensTyrosine-protein kinase JAK25.95.95.9pKd4