5TKD - chain B (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:9.2
Missing Residues:0
Missing Atoms:8
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:18.9Å
 
G-rich loop angle:52.2°
G-rich loop distance:14.6Å
G-rich loop rotation:69.7°
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I1
No H-bonds
I3
H-bond ligand
H-bond protein
I5
H-bond protein
I6
H-bond protein
I10
H-bond protein
Binding pocket sequence
UniprotSHLGQGTRTNVYEVVLKVLLAFYETASLMSQVTHLAFVHGVIMVTEYVEHGPLDVWLRRYLENKNLVHGNVCGRNILLLSDPGVG
Structure:SHLGQGTRTNVYEVVLKVLLAFYETASLMSQVTHLAFVHGVIMVTEYVEHGPLDVWLRRYLENKNLVHGNVCGRNILLLSDPGVG


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the 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 #
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  • COLORS
  • Interaction types
  • KLIFS (all res.)
  • KLIFS (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

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Binding affinities
ChEMBL ID:CHEMBL4279157
Bioaffinities: 6 records for 1 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensTyrosine-protein kinase TYK27.378.2pIC506