3OMV - chain B | Raf-1 proto-oncogene, serine/threonine kinase
Structure information
| PDB: | 3OMV |
| PubMed: | 20130576 |
| Release date: | 2010-09-15 |
| Resolution: | 4 Å |
| Kinase: | RAF1 |
| Family: | RAF |
| Group: | TKL |
| 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 (2.9Å) |
| ASP rotation (xDFG.81) : | 343° |
| PHE rotation (xDFG.82) : | 7° |
| Activation loop position: | -3.5Å |
| αC-helix position: | 18.8Å |
| G-rich loop angle: | 45.4° |
| G-rich loop distance: | 13.9Å |
| G-rich loop rotation: | 59.4° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
No waters were found in the defined clusters
Binding pocket sequence
| Uniprot | TRIGSGSFGTVYKVAVKILAFRNEVAVLRKTRVNILLFMGYAIVTQWCEGSSLYKHLHVYLHAKNIIHRDMKSNNIFLIGDFGLA |
| Structure: | TRIGSGSFGTVYKVAVKILAFRNEVAVLRKTRVNILLFMGYAIVTQWCEGSSLYKHLHVYLHAKNIIHRDMKSNNIFLIGDFGLA |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: SM5
Ligand Name: (1E)-5-(1-piperidin-4-yl-3-pyridin-4-yl-1H-pyrazol-4-yl)-2,3-dihydro-1H-inden-1-one oxime
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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 T 353 | 2 R 354 | 3 I 355 | 4 G 356 | 5 S 357 | 6 G 358 | 7 S 359 | 8 F 360 | 9 G 361 | 10 T 362 | 11 V 363 | 12 Y 364 | 13 K 365 | 14 V 372 | 15 A 373 | 16 V 374 | 17 K 375 | 18 I 376 | 19 L 377 | 20 A 389 |
| ■ | ■ | ■ | ■ | ■▲ | |||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 F 390 | 22 R 391 | 23 N 392 | 24 E 393 | 25 V 394 | 26 A 395 | 27 V 396 | 28 L 397 | 29 R 398 | 30 K 399 | 31 T 400 | 32 R 401 | 33 V 403 | 34 N 404 | 35 I 405 | 36 L 406 | 37 L 407 | 38 F 408 | 39 M 409 | 40 G 410 |
| ■ | |||||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 Y 411 | 42 A 418 | 43 I 419 | 44 V 420 | 45 T 421 | 46 Q 422 | 47 W 423 | 48 C 424 | 49 E 425 | 50 G 426 | 51 S 427 | 52 S 428 | 53 L 429 | 54 Y 430 | 55 K 431 | 56 H 432 | 57 L 433 | 58 H 434 | 59 V 435 | 60 Y 458 |
| ■ | ■ | ■▲ | ■ | ||||||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 L 459 | 62 H 460 | 63 A 461 | 64 K 462 | 65 N 463 | 66 I 464 | 67 I 465 | 68 H 466 | 69 R 467 | 70 D 468 | 71 M 469 | 72 K 470 | 73 S 471 | 74 N 472 | 75 N 473 | 76 I 474 | 77 F 475 | 78 L 476 | 79 I 484 | 80 G 485 |
| ■♦♦ | |||||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 486 | 82 F 487 | 83 G 488 | 84 L 489 | 85 A 490 | |||||||||||||||
Binding affinities
Ligand not found in ChEMBL.