3QUP - chain A | TYRO3 protein tyrosine kinase 3
Structure information
PDB: | 3QUP |
PubMed: | 22119469 |
Release date: | 2011-12-21 |
Resolution: | 1.9 Å |
Kinase: | Tyro3 (TYRO3) |
Family: | Axl |
Group: | TK |
Species: | MOUSE |
Quality Score: | 7.6 |
Missing Residues: | 1 |
Missing Atoms: | 0 |
DFG conformation: | out-like |
αC-helix conformation: | out |
Salt bridge KIII.17 and EαC.24: | No (10.7Å) |
ASP rotation (xDFG.81) : | 341° |
PHE rotation (xDFG.82) : | 352° |
Activation loop position: | -3.8Å |
αC-helix position: | 20.6Å |
G-rich loop angle: | 53° |
G-rich loop distance: | 16.6Å |
G-rich loop rotation: | 38° |
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
I4
H-bond protein
I5
H-bond protein
Binding pocket sequence
Uniprot | RMLGKGEFGSVREVAVKMLEFLREAACMKEFDPHVAKLVGVMVILPFMKHGDLHAFLLAYLSSRNFIHRDLAARNCMLVADFGLS |
Structure: | RMLGKGEFGSVREVAVKMLEFLREAACMKEFDPHVAKLVGVMVILPFMKHGDLHAFLLAYLSSRNFIHRDLAARNCMLVADFGL_ |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: LUN
Ligand Name: (5-fluoro-1H-indol-2-yl)[(3R)-1'-[(3R)-piperidin-3-yl]spiro[indole-3,3'-pyrrolidin]-1(2H)-yl]methanone
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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 517 | 7 E 518 | 8 F 519 | 9 G 520 | 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 E 554 |
■ | ■ | ■ | ■ | ■ | |||||||||||||||
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 L 666 | 85 _ _ | |||||||||||||||
■▲● |
Binding affinities
Ligand not found in ChEMBL.