4FF8 - chain A | TYRO3 protein tyrosine kinase 3
Structure information
PDB: | 4FF8 |
PubMed: | 23312472 |
Release date: | 2013-03-13 |
Resolution: | 2.4 Å |
Kinase: | Tyro3 (TYRO3) |
Family: | Axl |
Group: | TK |
Species: | MOUSE |
Quality Score: | 4 |
Missing Residues: | 37 |
Missing Atoms: | 0 |
DFG conformation: | na |
αC-helix conformation: | na |
Salt bridge KIII.17 and EαC.24: | NA |
ASP rotation (xDFG.81) : | ° |
PHE rotation (xDFG.82) : | 180° |
Activation loop position: | 0Å |
αC-helix position: | 0Å |
G-rich loop angle: | - |
G-rich loop distance: | - |
G-rich loop rotation: | - |
2D & 3D views
Binding pocket waters
No waters were found in the defined clusters
Binding pocket sequence
Uniprot | RMLGKGEFGSVREVAVKMLEFLREAACMKEFDPHVAKLVGVMVILPFMKHGDLHAFLLAYLSSRNFIHRDLAARNCMLVADFGLS |
Structure: | ____________________________KEFDPHVAKL____VILPFMKHGDLHAFLLAYLSSRNFIHRDLAARNCMLVA_____ |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: 14S
Ligand Name: 4-(cyclopentylamino)-2-[(2-methoxybenzyl)amino]-N-[3-(2-oxopyrrolidin-1-yl)propyl]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 _ _ | 2 _ _ | 3 _ _ | 4 _ _ | 5 _ _ | 6 _ _ | 7 _ _ | 8 _ _ | 9 _ _ | 10 _ _ | 11 _ _ | 12 _ _ | 13 _ _ | 14 _ _ | 15 _ _ | 16 _ _ | 17 _ _ | 18 _ _ | 19 _ _ | 20 _ _ |
αC | b.l | IV | |||||||||||||||||
21 _ _ | 22 _ _ | 23 _ _ | 24 _ _ | 25 _ _ | 26 _ _ | 27 _ _ | 28 _ _ | 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 _ _ | 40 _ _ |
■ | |||||||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 _ _ | 42 _ _ | 43 V 574 | 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 _ _ | 82 _ _ | 83 _ _ | 84 _ _ | 85 _ _ | |||||||||||||||
Binding affinities
ChEMBL ID:CHEMBL2312301Bioaffinities: 5 records for 4 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Hepatocyte growth factor receptor | 5.4 | 5.4 | 5.4 | pIC50 | 1 |
Homo sapiens | Proto-oncogene tyrosine-protein kinase MER | 5.3 | 5.3 | 5.3 | pIC50 | 1 |
Homo sapiens | Tyrosine-protein kinase receptor TYRO3 | 6.4 | 6.4 | 6.4 | pIC50 | 2 |
Homo sapiens | Tyrosine-protein kinase receptor UFO | 5.2 | 5.2 | 5.2 | pIC50 | 1 |