4GV1 - chain A (model A) | V-akt murine thymoma viral oncogene homolog 1
Structure information
PDB: | 4GV1 |
PubMed: | 23394218 |
Release date: | 2013-02-27 |
Resolution: | 1.49 Å |
Kinase: | AKT1 |
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 (2.5Å) |
ASP rotation (xDFG.81) : | 9° |
PHE rotation (xDFG.82) : | 1° |
Activation loop position: | -4.2Å |
αC-helix position: | 17.3Å |
G-rich loop angle: | 58.4° |
G-rich loop distance: | 17.8Å |
G-rich loop rotation: | 59° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
I3
H-bond ligand
H-bond protein
I5
H-bond protein
I11
H-bond protein
Binding pocket sequence
Uniprot | KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVMEYANGGELFFHLSRLHSEKNVVYRDLKLENLMLITDFGLC |
Structure: | KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVMEYANGGELFFHLSRLHSEKNVVYRDLKLENLMLITDFGLC |
Modified residues
Residue 308 (not in pocket)
Phosphorylated threonine
Orthosteric ligand
Ligand HET-code: 0XZ
Ligand Name: 4-amino-N-[(1S)-1-(4-chlorophenyl)-3-hydroxypropyl]-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidine-4-carboxamide
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- LABELS
- KLIFS residue #
- Amino Acid
- None
- COLORS
- Interaction types
- KLIFS (all res.)
- KLIFS (interacting res.)
- None
- OTHER
- Show/hide non-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 154 | 2 L 155 | 3 L 156 | 4 G 157 | 5 K 158 | 6 G 159 | 7 T 160 | 8 F 161 | 9 G 162 | 10 K 163 | 11 V 164 | 12 I 165 | 13 L 166 | 14 Y 176 | 15 A 177 | 16 M 178 | 17 K 179 | 18 I 180 | 19 L 181 | 20 H 194 |
■ | ■ | ■ | ■ | ■ | ■ | ■ | ■ | ■ | ■ | ||||||||||
αC | b.l | IV | |||||||||||||||||
21 T 195 | 22 L 196 | 23 T 197 | 24 E 198 | 25 N 199 | 26 R 200 | 27 V 201 | 28 L 202 | 29 Q 203 | 30 N 204 | 31 S 205 | 32 R 206 | 33 P 208 | 34 F 209 | 35 L 210 | 36 T 211 | 37 A 212 | 38 L 213 | 39 K 214 | 40 Y 215 |
■ | |||||||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 S 216 | 42 C 224 | 43 F 225 | 44 V 226 | 45 M 227 | 46 E 228 | 47 Y 229 | 48 A 230 | 49 N 231 | 50 G 232 | 51 G 233 | 52 E 234 | 53 L 235 | 54 F 236 | 55 F 237 | 56 H 238 | 57 L 239 | 58 S 240 | 59 R 241 | 60 L 264 |
■ | ▲ | ■♦ | ■▲ | ■▲ | |||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 H 265 | 62 S 266 | 63 E 267 | 64 K 268 | 65 N 269 | 66 V 270 | 67 V 271 | 68 Y 272 | 69 R 273 | 70 D 274 | 71 L 275 | 72 K 276 | 73 L 277 | 74 E 278 | 75 N 279 | 76 L 280 | 77 M 281 | 78 L 282 | 79 I 290 | 80 T 291 |
■ | ■ | ■ | ■ | ||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 292 | 82 F 293 | 83 G 294 | 84 L 295 | 85 C 296 | |||||||||||||||
■ |
Binding affinities
ChEMBL ID:CHEMBL2325741Bioaffinities: 34 records for 28 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | AMP-activated protein kinase, alpha-1 subunit | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | AMP-activated protein kinase, gamma-1 subunit | 5.6 | 5.6 | 5.6 | pKd | 1 |
Homo sapiens | AMP-activated protein kinase, gamma-2 subunit | 5.6 | 5.6 | 5.6 | pKd | 1 |
Homo sapiens | cAMP-dependent protein kinase alpha-catalytic subunit | 6.4 | 6.4 | 6.4 | pKd | 1 |
Homo sapiens | cAMP-dependent protein kinase beta-1 catalytic subunit | 6.6 | 6.6 | 6.6 | pKd | 1 |
Homo sapiens | cGMP-dependent protein kinase 1 beta | 6.5 | 6.5 | 6.5 | pKd | 1 |
Homo sapiens | Dual specificity protein kinase CLK4 | 6.3 | 6.3 | 6.3 | pKd | 1 |
Homo sapiens | Dual specificty protein kinase CLK1 | 6.3 | 6.3 | 6.3 | pKd | 1 |
Homo sapiens | Fibroblast growth factor receptor 1 | 6.1 | 6.1 | 6.1 | pKd | 1 |
Homo sapiens | G-protein coupled receptor kinase 2 | 5.3 | 5.3 | 5.3 | pKd | 1 |
Homo sapiens | LIM domain kinase 1 | 6.5 | 6.5 | 6.5 | pKd | 1 |
Homo sapiens | LIM domain kinase 2 | 6.3 | 6.3 | 6.3 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase 11 | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 3 | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | Protein kinase C alpha | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Protein kinase C beta | 5.6 | 5.6 | 5.6 | pKd | 1 |
Homo sapiens | Protein kinase C delta | 5.6 | 5.6 | 5.6 | pKd | 1 |
Homo sapiens | Protein kinase C nu | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | Protein kinase C theta | 5.4 | 5.4 | 5.4 | pKd | 1 |
Homo sapiens | Protein kinase N1 | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Rho-associated protein kinase 1 | 6.3 | 6.3 | 6.3 | pIC50 | 1 |
Homo sapiens | Rho-associated protein kinase 1 | 6.2 | 6.2 | 6.2 | pKd | 1 |
Homo sapiens | Rho-associated protein kinase 2 | 7.3 | 7.3 | 7.3 | pIC50 | 1 |
Homo sapiens | Rho-associated protein kinase 2 | 6.5 | 6.5 | 6.5 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase AKT | 7.6 | 7.5 | 8.5 | pIC50 | 3 |
Homo sapiens | Serine/threonine-protein kinase AKT | 5.4 | 5.4 | 5.4 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase AKT2 | 8.1 | 8.1 | 8.1 | pIC50 | 1 |
Homo sapiens | Serine/threonine-protein kinase AKT2 | 5.6 | 5.6 | 5.6 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase AKT3 | 8.1 | 8.1 | 8.1 | pIC50 | 1 |
Homo sapiens | Serine/threonine-protein kinase D2 | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase LATS1 | 4.9 | 4.9 | 4.9 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase receptor RET | 6 | 6 | 6 | pKd | 1 |