PDB-code
| Kinase structure | |
| Kinase: | LCK |
| Family: | Src |
| Group: | TK |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 2053 |
| PDB: | 3BYO |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2008-12-30 |
| PubMed: | 18278858 |
| Chain: | A |
| Orthosteric ligand: | AM9 |
 | |
| Structural information | |
| DFG conformation: | in |
| αC-helix conformation: | in |
| G-rich loop angle (distance): | 68° (20.8Å) |
| G-rich loop rotation: | 42.1° |
| Quality Score: | 8 |
| Resolution: | 2 Å |
| Missing Residues: | 0 |
| Missing Atoms: | 0 |
| Ligand binding mode | ||||
| Pockets | Subpockets | Waters | ||
| front gate back | BP-I-A BP-I-B | Cluster I1 I2 I3 I4 I5 I10 | Ligand No No No No No Yes | Protein Yes No No Yes Yes Yes |
| Pocket alignment | |
| Uniprot sequence: | ERLGAGQFGEVWMVAVKSLAFLAEANLMKQLQQRLVRLYAVYIITEYMENGSLVDFLKTFIEERNYIHRDLRAANILVIADFGLA |
| Sequence structure: | ERLGAGQFGEVWMVAVKSLAFLAEANLMKQLQQRLVRLYAVYIITEYMENGSLVDFLKTFIEERNYIHRDLRAANILVIADFGLA |
| Ligand affinity | |
| ChEMBL ID: | CHEMBL410295 |
| Bioaffinities: | 16 records for 13 kinases |
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | c-Jun N-terminal kinase 3 | 5.1 | 5.1 | 5.1 | pIC50 | 1 |
| Homo sapiens | Serine/threonine-protein kinase B-raf | 6.3 | 6.3 | 6.3 | pIC50 | 1 |
| Homo sapiens | Stem cell growth factor receptor | 6.3 | 6.3 | 6.3 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase BTK | 6.4 | 6.4 | 6.4 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase JAK3 | 6.8 | 6.8 | 6.8 | pIC50 | 2 |
| Homo sapiens | Tyrosine-protein kinase LCK | 5.8 | 5.8 | 8.2 | pIC50 | 2 |
| Homo sapiens | Tyrosine-protein kinase Lyn | 7.7 | 7.7 | 7.7 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase SRC | 6.9 | 6.9 | 6.9 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase SYK | 6.7 | 6.7 | 6.7 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase TIE-2 | 6.1 | 6.1 | 6.1 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase TYK2 | 5.9 | 5.9 | 5.9 | pIC50 | 2 |
| Homo sapiens | Tyrosine-protein kinase ZAP-70 | 5.8 | 5.8 | 5.8 | pIC50 | 1 |
| Homo sapiens | Vascular endothelial growth factor receptor 2 | 5.3 | 5.3 | 5.3 | pIC50 | 1 |
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 249 | 2 R 250 | 3 L 251 | 4 G 252 | 5 A 253 | 6 G 254 | 7 Q 255 | 8 F 256 | 9 G 257 | 10 E 258 | 11 V 259 | 12 W 260 | 13 M 261 | 14 V 270 | 15 A 271 | 16 V 272 | 17 K 273 | 18 S 274 | 19 L 275 | 20 A 284 |
| • | • | • | • | • | • | ||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 F 285 | 22 L 286 | 23 A 287 | 24 E 288 | 25 A 289 | 26 N 290 | 27 L 291 | 28 M 292 | 29 K 293 | 30 Q 294 | 31 L 295 | 32 Q 296 | 33 Q 298 | 34 R 299 | 35 L 300 | 36 V 301 | 37 R 302 | 38 L 303 | 39 Y 304 | 40 A 305 |
| • | |||||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 V 306 | 42 Y 313 | 43 I 314 | 44 I 315 | 45 T 316 | 46 E 317 | 47 Y 318 | 48 M 319 | 49 E 320 | 50 N 321 | 51 G 322 | 52 S 323 | 53 L 324 | 54 V 325 | 55 D 326 | 56 F 327 | 57 L 328 | 58 K 329 | 59 T 330 | 60 F 354 |
| • | •• | • | •• | ••• | • | • | |||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 I 355 | 62 E 356 | 63 E 357 | 64 R 358 | 65 N 359 | 66 Y 360 | 67 I 361 | 68 H 362 | 69 R 363 | 70 D 364 | 71 L 365 | 72 R 366 | 73 A 367 | 74 A 368 | 75 N 369 | 76 I 370 | 77 L 371 | 78 V 372 | 79 I 380 | 80 A 381 |
| • | • | ||||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 382 | 82 F 383 | 83 G 384 | 84 L 385 | 85 A 386 | |||||||||||||||
| • | |||||||||||||||||||
Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
