6BTW - chain A (model A) | Vaccinia related kinase 1
Structure information
PDB:6BTW
PubMed:-
Release date:2017-12-20
Resolution:1.9 Å
 
Kinase:VRK1
Family:VRK
Group:CK1
Species:HUMAN
 
Quality Score:7.3
Missing Residues:5
Missing Atoms:7
DFG conformation:in
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (2.8Å)
 
 
ASP rotation (xDFG.81) :348°
PHE rotation (xDFG.82) :21°
Activation loop position:-3.1Å
αC-helix position:17.7Å
 
G-rich loop angle:-
G-rich loop distance:-
G-rich loop rotation:-
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
No waters were found in the defined clusters
Binding pocket sequence
UniprotLPIGQGGFGCIYLCVVKVEPLFTELKFYQRAALGVPKYWGSFMIMDRFG-SDLQKIYEAYIHEHEYVHGDIKASNLLLLVDYGLA
Structure:LPIG_____CIYLCVVKVEPLFTELKFYQRAALGVPKYWGSFMIMDRFG_SDLQKIYEAYIHEHEYVHGDIKASNLLLLVDYGLA


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: E8D
Ligand Name: 2-[(3,5-difluoro-4-hydroxyphenyl)amino]-8-phenyl-7,8-dihydropteridin-6(5H)-one

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  • LABELS
  • KLIFS residue #
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  • None
  • 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 L
41
2 P
42
3 I
43
4 G
49
5 _
_
6 _
_
7 _
_
8 _
_
9 _
_
10 C
50
11 I
51
12 Y
52
13 L
53
14 C
68
15 V
69
16 V
70
17 K
71
18 V
72
19 E
73
20 P
79
αC b.l IV
21 L
80
22 F
81
23 T
82
24 E
83
25 L
84
26 K
85
27 F
86
28 Y
87
29 Q
88
30 R
89
31 A
90
32 A
91
33 L
108
34 G
109
35 V
110
36 P
111
37 K
112
38 Y
113
39 W
114
40 G
115
IV V GK hinge linker αD αE
41 S
116
42 F
128
43 M
129
44 I
130
45 M
131
46 D
132
47 R
133
48 F
134
49 G
135
50 _
_
51 S
136
52 D
137
53 L
138
54 Q
139
55 K
140
56 I
141
57 Y
142
58 E
143
59 A
144
60 Y
167
αE VI c.l VII VIII x
61 I
168
62 H
169
63 E
170
64 H
171
65 E
172
66 Y
173
67 V
174
68 H
175
69 G
176
70 D
177
71 I
178
72 K
179
73 A
180
74 S
181
75 N
182
76 L
183
77 L
184
78 L
185
79 L
195
80 V
196
DFG a.l
81 D
197
82 Y
198
83 G
199
84 L
200
85 A
201

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Binding affinities
Ligand not found in ChEMBL.