5TKD - chain A (model B) | Tyrosine kinase 2 (2nd domain)
Structure information
PDB: | 5TKD |
PubMed: | 30108788 |
Release date: | 2016-12-28 |
Resolution: | 1.92 Å |
Kinase: | TYK2-b |
Family: | JakB |
Group: | TK |
Species: | HUMAN |
Quality Score: | 8.5 |
Missing Residues: | 0 |
Missing Atoms: | 15 |
DFG conformation: | in |
αC-helix conformation: | in |
Salt bridge KIII.17 and EαC.24: | No |
ASP rotation (xDFG.81) : | 86° |
PHE rotation (xDFG.82) : | 20° |
Activation loop position: | -3.6Å |
αC-helix position: | 18.7Å |
G-rich loop angle: | 52.3° |
G-rich loop distance: | 14.7Å |
G-rich loop rotation: | 69.5° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I5
H-bond protein
I6
H-bond ligand
H-bond protein
I10
H-bond protein
Binding pocket sequence
Uniprot | SHLGQGTRTNVYEVVLKVLLAFYETASLMSQVTHLAFVHGVIMVTEYVEHGPLDVWLRRYLENKNLVHGNVCGRNILLLSDPGVG |
Structure: | SHLGQGTRTNVYEVVLKVLLAFYETASLMSQVTHLAFVHGVIMVTEYVEHGPLDVWLRRYLENKNLVHGNVCGRNILLLSDPGVG |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: 7GL
Ligand Name: 6-[(3,5-dimethylphenyl)amino]-8-(methylamino)imidazo[1,2-b]pyridazine-3-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.
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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 S 593 | 2 H 594 | 3 L 595 | 4 G 596 | 5 Q 597 | 6 G 598 | 7 T 599 | 8 R 600 | 9 T 601 | 10 N 602 | 11 V 603 | 12 Y 604 | 13 E 605 | 14 V 639 | 15 V 640 | 16 L 641 | 17 K 642 | 18 V 643 | 19 L 644 | 20 L 653 |
■ | ■ | ■ | ■ | ■ | ■▲ | ||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 A 654 | 22 F 655 | 23 Y 656 | 24 E 657 | 25 T 658 | 26 A 659 | 27 S 660 | 28 L 661 | 29 M 662 | 30 S 663 | 31 Q 664 | 32 V 665 | 33 T 668 | 34 H 669 | 35 L 670 | 36 A 671 | 37 F 672 | 38 V 673 | 39 H 674 | 40 G 675 |
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 V 676 | 42 I 684 | 43 M 685 | 44 V 686 | 45 T 687 | 46 E 688 | 47 Y 689 | 48 V 690 | 49 E 691 | 50 H 692 | 51 G 693 | 52 P 694 | 53 L 695 | 54 D 696 | 55 V 697 | 56 W 698 | 57 L 699 | 58 R 700 | 59 R 701 | 60 Y 724 |
■ | ■ | ■▲▲ | ■ | ■ | ■ | ■ | ■ | ||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 L 725 | 62 E 726 | 63 N 727 | 64 K 728 | 65 N 729 | 66 L 730 | 67 V 731 | 68 H 732 | 69 G 733 | 70 N 734 | 71 V 735 | 72 C 736 | 73 G 737 | 74 R 738 | 75 N 739 | 76 I 740 | 77 L 741 | 78 L 742 | 79 L 757 | 80 S 758 |
■ | ■ | ||||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 759 | 82 P 760 | 83 G 761 | 84 V 762 | 85 G 763 | |||||||||||||||
Binding affinities
ChEMBL ID:CHEMBL4279157Bioaffinities: 6 records for 1 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Tyrosine-protein kinase TYK2 | 7.3 | 7 | 8.2 | pIC50 | 6 |