3E8D - chain B (model A) | V-akt murine thymoma viral oncogene homolog 2
Structure information
PDB: | 3E8D |
PubMed: | 19179070 |
Release date: | 2008-10-14 |
Resolution: | 2.7 Å |
Kinase: | AKT2 |
Family: | Akt |
Group: | AGC |
Species: | HUMAN |
Quality Score: | 9.4 |
Missing Residues: | 0 |
Missing Atoms: | 6 |
DFG conformation: | in |
αC-helix conformation: | in |
Salt bridge KIII.17 and EαC.24: | Yes (2.9Å) |
ASP rotation (xDFG.81) : | 338° |
PHE rotation (xDFG.82) : | 359° |
Activation loop position: | -3.9Å |
αC-helix position: | 17.5Å |
G-rich loop angle: | 58.1° |
G-rich loop distance: | 17.9Å |
G-rich loop rotation: | 52.3° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
No waters were found in the defined clusters
Binding pocket sequence
Uniprot | KLLGKGTFGKVILYAMKILHTVTESRVLQNTRPFLTALKYACFVMEYANGGELFFHLSRYLHSRDVVYRDIKLENLMLITDFGLC |
Structure: | KLLGKGTFGKVILYAMKILHTVTESRVLQNTRPFLTALKYACFVMEYANGGELFFHLSRYLHSRDVVYRDIKLENLMLITDFGLC |
Modified residues
Residue 309 (not in pocket)
Phosphorylated threonine
Orthosteric ligand
Ligand HET-code: G98
Ligand Name: 4-[2-(4-amino-2,5-dihydro-1,2,5-oxadiazol-3-yl)-6-{[(1S)-3-amino-1-phenylpropyl]oxy}-1-ethyl-1H-imidazo[4,5-c]pyridin-4-yl]-2-methylbut-3-yn-2-ol
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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 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 | |||||||||||||||
■▲ | ■ |
Binding affinities
ChEMBL ID:CHEMBL1099297Bioaffinities: 5 records for 3 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Glycogen synthase kinase-3 beta | 7.4 | 7.4 | 7.4 | pIC50 | 1 |
Homo sapiens | Serine/threonine-protein kinase AKT | 8.7 | 8.7 | 8.7 | pIC50 | 1 |
Homo sapiens | Serine/threonine-protein kinase AKT | 9.7 | 9.7 | 9.7 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase AKT2 | 7.8 | 7.8 | 7.8 | pIC50 | 1 |
Homo sapiens | Serine/threonine-protein kinase AKT2 | 9 | 9 | 9 | pKi | 1 |