3LXP - chain A | Tyrosine kinase 2
Structure information
PDB:3LXP
PubMed:20478313
Release date:2010-06-02
Resolution:1.65 Å
 
Kinase:TYK2
Family:JakA
Group:TK
Species:HUMAN
 
Quality Score:8
Missing Residues:0
Missing Atoms:25
DFG conformation:in
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (2.6Å)
 
 
ASP rotation (xDFG.81) :358°
PHE rotation (xDFG.82) :14°
Activation loop position:-3.4Å
αC-helix position:17.7Å
 
G-rich loop angle:46.8°
G-rich loop distance:14.4Å
G-rich loop rotation:63°
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
I2
H-bond ligand
I4
H-bond protein
I5
H-bond ligand
H-bond protein
Binding pocket sequence
UniprotRDLGEGHFGKVSLVAVKALGWKQEIDILRTLYEHIIKYKGCQLVMEYVPLGSLRDYLPRYLHAQHYIHRDLAARNVLLIGDFGLA
Structure:RDLGEGHFGKVSLVAVKALGWKQEIDILRTLYEHIIKYKGCQLVMEYVPLGSLRDYLPRYLHAQHYIHRDLAARNVLLIGDFGLA


Modified residues
Residue 1054 (not in pocket)
Phosphorylated tyrosine
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: IZA
Ligand Name: 2-TERT-BUTYL-9-FLUORO-3,6-DIHYDRO-7H-BENZ[H]-IMIDAZ[4,5-F]ISOQUINOLINE-7-ONE

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  • KLIFS residue #
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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
901
2 D
902
3 L
903
4 G
904
5 E
905
6 G
906
7 H
907
8 F
908
9 G
909
10 K
910
11 V
911
12 S
912
13 L
913
14 V
927
15 A
928
16 V
929
17 K
930
18 A
931
19 L
932
20 G
943
αC b.l IV
21 W
944
22 K
945
23 Q
946
24 E
947
25 I
948
26 D
949
27 I
950
28 L
951
29 R
952
30 T
953
31 L
954
32 Y
955
33 E
957
34 H
958
35 I
959
36 I
960
37 K
961
38 Y
962
39 K
963
40 G
964
IV V GK hinge linker αD αE
41 C
965
42 Q
975
43 L
976
44 V
977
45 M
978
46 E
979
47 Y
980
48 V
981
49 P
982
50 L
983
51 G
984
52 S
985
53 L
986
54 R
987
55 D
988
56 Y
989
57 L
990
58 P
991
59 R
992
60 Y
1013
αE VI c.l VII VIII x
61 L
1014
62 H
1015
63 A
1016
64 Q
1017
65 H
1018
66 Y
1019
67 I
1020
68 H
1021
69 R
1022
70 D
1023
71 L
1024
72 A
1025
73 A
1026
74 R
1027
75 N
1028
76 V
1029
77 L
1030
78 L
1031
79 I
1039
80 G
1040
DFG a.l
81 D
1041
82 F
1042
83 G
1043
84 L
1044
85 A
1045

Interaction pattern search
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Binding affinities
ChEMBL ID:CHEMBL21156
Bioaffinities: 86 records for 45 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensALK tyrosine kinase receptor6.86.86.8pKi1
Homo sapiensAMP-activated protein kinase, alpha-1 subunit6.86.86.8pKi1
Homo sapienscAMP-dependent protein kinase alpha-catalytic subunit6.36.36.3pKi1
Homo sapiensc-Jun N-terminal kinase 17.87.87.8pKi1
Homo sapiensc-Jun N-terminal kinase 27.17.17.1pKi1
Homo sapiensCyclin-dependent kinase 25.55.55.5pIC501
Homo sapiensDeath-associated protein kinase 3999pKi1
Homo sapiensDual specificity mitogen-activated protein kinase kinase 1777pKi1
Homo sapiensDual specificity mitogen-activated protein kinase kinase 26.46.46.4pKi1
Homo sapiensDual specificity protein kinase CLK47.17.17.1pKi1
Homo sapiensFibroblast growth factor receptor 2666pIC501
Homo sapiensFocal adhesion kinase 16.16.16.1pKi1
Homo sapiensG protein-coupled receptor kinase 56.46.46.4pKi1
Homo sapiensInhibitor of nuclear factor kappa B kinase beta subunit6.56.56.5pIC501
Homo sapiensInhibitor of nuclear factor kappa B kinase epsilon subunit777pKi1
Homo sapiensLeucine-rich repeat serine/threonine-protein kinase 27.67.67.6pKi1
Homo sapiensLeukocyte tyrosine kinase receptor7.67.67.6pKi1
Homo sapiensMacrophage-stimulating protein receptor7.57.57.5pKi1
Homo sapiensMaternal embryonic leucine zipper kinase6.56.56.5pIC501
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 25.65.65.6pKi1
Homo sapiensNeurotrophic tyrosine kinase receptor type 2666pKi1
Homo sapiensNT-3 growth factor receptor5.55.55.5pKi1
Homo sapiensProtein kinase C alpha5.95.95.9pIC501
Homo sapiensProtein kinase C nu7.17.17.1pKi1
Homo sapiensProtein kinase C theta6.16.16.1pKi1
Homo sapiensRho-associated protein kinase 16.36.36.3pKi1
Homo sapiensRibosomal protein S6 kinase alpha 36.46.46.4pKi2
Homo sapiensSerine/threonine-protein kinase Aurora-B7.37.37.3pKi1
Homo sapiensSerine/threonine-protein kinase Chk15.55.55.5pKi1
Homo sapiensSerine/threonine-protein kinase PIM16.26.26.2pKi1
Homo sapiensSerine/threonine-protein kinase TBK16.76.76.7pKi1
Homo sapiensTyrosine kinase non-receptor protein 26.96.96.9pKi1
Homo sapiensTyrosine-protein kinase CSK5.75.75.7pIC501
Homo sapiensTyrosine-protein kinase FYN6.36.36.3pIC501
Homo sapiensTyrosine-protein kinase HCK5.15.15.1pIC501
Homo sapiensTyrosine-protein kinase JAK17.86.28.4pIC506
Mus musculusTyrosine-protein kinase JAK17.87.87.8pIC504
Homo sapiensTyrosine-protein kinase JAK295.99pIC5010
Homo sapiensTyrosine-protein kinase JAK28.68.68.6pKi2
Homo sapiensTyrosine-protein kinase JAK38.36.18.3pIC5010
Homo sapiensTyrosine-protein kinase JAK37.47.47.4pKi2
Homo sapiensTyrosine-protein kinase receptor RET6.76.76.7pKi1
Homo sapiensTyrosine-protein kinase TIE-24.64.64.6pIC501
Homo sapiensTyrosine-protein kinase TYK295.89pIC5010
Homo sapiensVascular endothelial growth factor receptor 15.85.85.8pIC501
Homo sapiensVascular endothelial growth factor receptor 25.95.95.9pIC501
Homo sapiensVascular endothelial growth factor receptor 25.85.85.8pKi1
Homo sapiensVascular endothelial growth factor receptor 36.26.26.2pIC501