4D9U - chain A | Ribosomal protein S6 kinase A3 (2nd domain)
Structure information
| PDB: | 4D9U |
| PubMed: | 22466421 |
| Release date: | 2012-04-11 |
| Resolution: | 2.4 Å |
| Kinase: | RPS6KA3-b (RSK2-b) |
| Family: | RSKb |
| Group: | CAMK |
| 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 (3.1Å) |
| ASP rotation (xDFG.81) : | 3° |
| PHE rotation (xDFG.82) : | 14° |
| Activation loop position: | -4.5Å |
| αC-helix position: | 17.4Å |
| G-rich loop angle: | 53.4° |
| G-rich loop distance: | 16.7Å |
| G-rich loop rotation: | 42.1° |
2D & 3D views
Binding pocket waters
No waters were found in the defined clusters
Binding pocket sequence
| Uniprot | EDIGVGSYSVCKRFAVKIIDPTEEIEILLRYGPNIITLKDVYVVTELMKGGELLDKILRYLHAQGVVHRDLKPSNILYICDFGFA |
| Structure: | EDIGVGSYSVCKRFAVKIIDPTEEIEILLRYGPNIITLKDVYVVTELMKGGELLDKILRYLHAQGVVHRDLKPSNILYICDFGFA |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: 0JH
Ligand Name: tert-butyl (2S)-3-[4-amino-7-(3-hydroxypropyl)-5-(4-methylphenyl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]-2-cyanopropanoate
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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 E 426 | 2 D 427 | 3 I 428 | 4 G 429 | 5 V 430 | 6 G 431 | 7 S 432 | 8 Y 433 | 9 S 434 | 10 V 435 | 11 C 436 | 12 K 437 | 13 R 438 | 14 F 448 | 15 A 449 | 16 V 450 | 17 K 451 | 18 I 452 | 19 I 453 | 20 D 459 |
| ■▲ | ■ | ■ | ■ | ■ | ■ | ■ | ■ | ■ | ■ | ||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 P 460 | 22 T 461 | 23 E 462 | 24 E 463 | 25 I 464 | 26 E 465 | 27 I 466 | 28 L 467 | 29 L 468 | 30 R 469 | 31 Y 470 | 32 G 471 | 33 P 474 | 34 N 475 | 35 I 476 | 36 I 477 | 37 T 478 | 38 L 479 | 39 K 480 | 40 D 481 |
| ■ | ■ | ||||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 V 482 | 42 Y 490 | 43 V 491 | 44 V 492 | 45 T 493 | 46 E 494 | 47 L 495 | 48 M 496 | 49 K 497 | 50 G 498 | 51 G 499 | 52 E 500 | 53 L 501 | 54 L 502 | 55 D 503 | 56 K 504 | 57 I 505 | 58 L 506 | 59 R 507 | 60 Y 529 |
| ■ | ■▲ | ▲ | ■ | ■▲ | |||||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 L 530 | 62 H 531 | 63 A 532 | 64 Q 533 | 65 G 534 | 66 V 535 | 67 V 536 | 68 H 537 | 69 R 538 | 70 D 539 | 71 L 540 | 72 K 541 | 73 P 542 | 74 S 543 | 75 N 544 | 76 I 545 | 77 L 546 | 78 Y 547 | 79 I 559 | 80 C 560 |
| ■ | ■ | ||||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 561 | 82 F 562 | 83 G 563 | 84 F 564 | 85 A 565 | |||||||||||||||
| ■ | |||||||||||||||||||
Binding affinities
Ligand not found in ChEMBL.