3KF4 - chain A | C-abl oncogene 1, non-receptor tyrosine kinase
Structure information
| PDB: | 3KF4 |
| PubMed: | 19895503 |
| Release date: | 2009-12-22 |
| Resolution: | 1.9 Å |
| Kinase: | Abl1 (ABL1) |
| Family: | Abl |
| Group: | TK |
| Species: | MOUSE |
| 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) : | 334° |
| PHE rotation (xDFG.82) : | 4° |
| Activation loop position: | -3.3Å |
| αC-helix position: | 17.3Å |
| G-rich loop angle: | 59.7° |
| G-rich loop distance: | 18.1Å |
| G-rich loop rotation: | 8.7° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I2
H-bond protein
I3
H-bond protein
I10
H-bond ligand
H-bond protein
Binding pocket sequence
| Uniprot | HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS |
| Structure: | HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: B90
Ligand Name: N-[4-(dimethylphosphoryl)phenyl]-9-[(E)-2-(5-methyl-1H-indazol-4-yl)ethenyl]-9H-purin-6-amine
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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.
- En/disable resizing interacting res.
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 H 246 | 2 K 247 | 3 L 248 | 4 G 249 | 5 G 250 | 6 G 251 | 7 Q 252 | 8 Y 253 | 9 G 254 | 10 E 255 | 11 V 256 | 12 Y 257 | 13 E 258 | 14 V 268 | 15 A 269 | 16 V 270 | 17 K 271 | 18 T 272 | 19 L 273 | 20 E 282 |
| ■ | ■♦ | ■ | ■ | ■ | ■ | ||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 F 283 | 22 L 284 | 23 K 285 | 24 E 286 | 25 A 287 | 26 A 288 | 27 V 289 | 28 M 290 | 29 K 291 | 30 E 292 | 31 I 293 | 32 K 294 | 33 P 296 | 34 N 297 | 35 L 298 | 36 V 299 | 37 Q 300 | 38 L 301 | 39 L 302 | 40 G 303 |
| ■▲ | ■ | ■ | |||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 V 304 | 42 Y 312 | 43 I 313 | 44 I 314 | 45 T 315 | 46 E 316 | 47 F 317 | 48 M 318 | 49 T 319 | 50 Y 320 | 51 G 321 | 52 N 322 | 53 L 323 | 54 L 324 | 55 D 325 | 56 Y 326 | 57 L 327 | 58 R 328 | 59 E 329 | 60 Y 353 |
| ■ | ■ | ■ | ■♦ | ■▲▲ | ■ | ■ | ■ | ||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 L 354 | 62 E 355 | 63 K 356 | 64 K 357 | 65 N 358 | 66 F 359 | 67 I 360 | 68 H 361 | 69 R 362 | 70 D 363 | 71 L 364 | 72 A 365 | 73 A 366 | 74 R 367 | 75 N 368 | 76 C 369 | 77 L 370 | 78 V 371 | 79 V 379 | 80 A 380 |
| ■ | ■ | ||||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 381 | 82 F 382 | 83 G 383 | 84 L 384 | 85 S 385 | |||||||||||||||
| ▲ | |||||||||||||||||||
Binding affinities
ChEMBL ID:CHEMBL510893Bioaffinities: No (p)Ki/(p)IC50/(p)EC50 values for kinases found (with a ChEMBL confidence ≥ 8).