4FEQ - chain A | TYRO3 protein tyrosine kinase 3
Structure information
| PDB: | 4FEQ |
| PubMed: | 23312472 |
| Release date: | 2013-03-13 |
| Resolution: | 2.2 Å |
| Kinase: | Tyro3 (TYRO3) |
| Family: | Axl |
| Group: | TK |
| Species: | MOUSE |
| Quality Score: | 5.6 |
| Missing Residues: | 6 |
| Missing Atoms: | 0 |
| DFG conformation: | in |
| αC-helix conformation: | out |
| Salt bridge KIII.17 and EαC.24: | No (11.6Å) |
| ASP rotation (xDFG.81) : | 342° |
| PHE rotation (xDFG.82) : | 346° |
| Activation loop position: | -3.6Å |
| αC-helix position: | 21.2Å |
| G-rich loop angle: | - |
| G-rich loop distance: | - |
| G-rich loop rotation: | - |
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
Binding pocket sequence
| Uniprot | RMLGKGEFGSVREVAVKMLEFLREAACMKEFDPHVAKLVGVMVILPFMKHGDLHAFLLAYLSSRNFIHRDLAARNCMLVADFGLS |
| Structure: | RMLGKG___SVREVAVKML_FLREAACMKEFDPHVAKLVGVMVILPFMKHGDLHAFLLAYLSSRNFIHRDLAARNCMLVADFG__ |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: 0T8
Ligand Name: 4-(cyclopentylamino)-N-[3-(2-oxopyrrolidin-1-yl)propyl]-2-{[2-(pyridin-4-yl)ethyl]amino}pyrimidine-5-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.
- 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 R 512 | 2 M 513 | 3 L 514 | 4 G 515 | 5 K 516 | 6 G 520 | 7 _ _ | 8 _ _ | 9 _ _ | 10 S 521 | 11 V 522 | 12 R 523 | 13 E 524 | 14 V 537 | 15 A 538 | 16 V 539 | 17 K 540 | 18 M 541 | 19 L 542 | 20 _ _ |
| ■ | ■ | ■ | ■ | ■ | |||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 F 555 | 22 L 556 | 23 R 557 | 24 E 558 | 25 A 559 | 26 A 560 | 27 C 561 | 28 M 562 | 29 K 563 | 30 E 564 | 31 F 565 | 32 D 566 | 33 P 568 | 34 H 569 | 35 V 570 | 36 A 571 | 37 K 572 | 38 L 573 | 39 V 574 | 40 G 575 |
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 V 576 | 42 M 590 | 43 V 591 | 44 I 592 | 45 L 593 | 46 P 594 | 47 F 595 | 48 M 596 | 49 K 597 | 50 H 598 | 51 G 599 | 52 D 600 | 53 L 601 | 54 H 602 | 55 A 603 | 56 F 604 | 57 L 605 | 58 L 606 | 59 A 607 | 60 Y 635 |
| ■ | ▲ | ■♦ | ■▲▲ | ■ | ■ | ■ | ■ | ||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 L 636 | 62 S 637 | 63 S 638 | 64 R 639 | 65 N 640 | 66 F 641 | 67 I 642 | 68 H 643 | 69 R 644 | 70 D 645 | 71 L 646 | 72 A 647 | 73 A 648 | 74 R 649 | 75 N 650 | 76 C 651 | 77 M 652 | 78 L 653 | 79 V 661 | 80 A 662 |
| ■ | |||||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 663 | 82 F 664 | 83 G 665 | 84 _ _ | 85 _ _ | |||||||||||||||
| ■ | |||||||||||||||||||
Binding affinities
ChEMBL ID:CHEMBL2312308Bioaffinities: 1 record for 1 kinase(s)
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | Tyrosine-protein kinase receptor TYRO3 | 6 | 6 | 6 | pIC50 | 1 |