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

The orthosteric binding pocket
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
UniprotRMLGKGEFGSVREVAVKMLEFLREAACMKEFDPHVAKLVGVMVILPFMKHGDLHAFLLAYLSSRNFIHRDLAARNCMLVADFGLS
Structure:RMLGKGEFGSVREVAVKMLEFLREAACMKEFDPHVAKLVGVMVILPFMKHGDLHAFLLAYLSSRNFIHRDLAARNCMLVADFGL_


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the 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 #
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  • COLORS
  • Interaction types
  • KLIFS (all res.)
  • KLIFS (interacting res.)
  • None
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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 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 _
_

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Binding affinities
Ligand not found in ChEMBL.