6VNS - chain A (model A) | Tyrosine kinase 2
Structure information
PDB:6VNS
PubMed:32253095
Release date:2020-04-08
Resolution:2.09 Å
 
Kinase:TYK2
Family:JakA
Group:TK
Species:HUMAN
 
Quality Score:8
Missing Residues:0
Missing Atoms:0
DFG conformation:in
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (2.8Å)
 
 
ASP rotation (xDFG.81) :10°
PHE rotation (xDFG.82) :13°
Activation loop position:-4.9Å
αC-helix position:18.6Å
 
G-rich loop angle:51°
G-rich loop distance:15.9Å
G-rich loop rotation:55°
Other models from this PDB:
2D & 3D views

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


Modified residues
Residue 1054 (not in pocket)
Phosphorylated tyrosine
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: R5D
Ligand Name: (1R,2R)-2-cyano-N-[(1S,5R)-3-(5-fluoro-2-{[1-(2-hydroxyethyl)-1H-pyrazol-4-yl]amino}pyrimidin-4-yl)-3-azabicyclo[3.1.0]hexan-1-yl]cyclopropane-1-carboxamide

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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 S
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:CHEMBL4644138
Bioaffinities: 8 records for 4 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensTyrosine-protein kinase JAK17.87.87.8pIC502
Homo sapiensTyrosine-protein kinase JAK26.56.56.5pIC502
Homo sapiensTyrosine-protein kinase JAK3666pIC502
Homo sapiensTyrosine-protein kinase TYK27.57.57.5pIC502