2X39 - chain A | V-akt murine thymoma viral oncogene homolog 2
Structure information
PDB:2X39
PubMed:20151677
Release date:2010-02-23
Resolution:1.93 Å
 
Kinase:AKT2
Family:Akt
Group:AGC
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 (2.8Å)
 
 
ASP rotation (xDFG.81) :353°
PHE rotation (xDFG.82) :
Activation loop position:-3.9Å
αC-helix position:17.6Å
 
G-rich loop angle:57.5°
G-rich loop distance:17.3Å
G-rich loop rotation:60.6°
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
Binding pocket sequence
UniprotKLLGKGTFGKVILYAMKILHTVTESRVLQNTRPFLTALKYACFVMEYANGGELFFHLSRYLHSRDVVYRDIKLENLMLITDFGLC
Structure:KLLGKGTFGKVILYAMKILHTVTESRVLQNTRPFLTALKYACFVMEYANGGELFFHLSRYLHSRDVVYRDIKLENLMLITDFGLC


Modified residues
Residue 309 (not in pocket)
Phosphorylated threonine
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: X39
Ligand Name: 4-AMINO-N-(4-CHLOROBENZYL)-1-(7H-PYRROLO[2,3-D]PYRIMIDIN-4-YL)PIPERIDINE-4-CARBOXAMIDE

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  • LABELS
  • KLIFS residue #
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  • COLORS
  • Interaction types
  • KLIFS (all res.)
  • KLIFS (interacting res.)
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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 K
156
2 L
157
3 L
158
4 G
159
5 K
160
6 G
161
7 T
162
8 F
163
9 G
164
10 K
165
11 V
166
12 I
167
13 L
168
14 Y
178
15 A
179
16 M
180
17 K
181
18 I
182
19 L
183
20 H
196
αC b.l IV
21 T
197
22 V
198
23 T
199
24 E
200
25 S
201
26 R
202
27 V
203
28 L
204
29 Q
205
30 N
206
31 T
207
32 R
208
33 P
210
34 F
211
35 L
212
36 T
213
37 A
214
38 L
215
39 K
216
40 Y
217
IV V GK hinge linker αD αE
41 A
218
42 C
226
43 F
227
44 V
228
45 M
229
46 E
230
47 Y
231
48 A
232
49 N
233
50 G
234
51 G
235
52 E
236
53 L
237
54 F
238
55 F
239
56 H
240
57 L
241
58 S
242
59 R
243
60 Y
265
αE VI c.l VII VIII x
61 L
266
62 H
267
63 S
268
64 R
269
65 D
270
66 V
271
67 V
272
68 Y
273
69 R
274
70 D
275
71 I
276
72 K
277
73 L
278
74 E
279
75 N
280
76 L
281
77 M
282
78 L
283
79 I
291
80 T
292
DFG a.l
81 D
293
82 F
294
83 G
295
84 L
296
85 C
297

Interaction pattern search
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Binding affinities
ChEMBL ID:CHEMBL598194
Bioaffinities: 6 records for 4 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensRho-associated protein kinase 26.86.87.2pIC502
Homo sapiensSerine/threonine-protein kinase AKT7.97.97.9pIC501
Homo sapiensSerine/threonine-protein kinase AKT27.27.28.7pIC502
Homo sapiensSerine/threonine-protein kinase AKT37.27.27.2pIC501