6VRF - chain B (model A) | Tau tubulin kinase 2
Structure information
PDB:6VRF
PubMed:32424773
Release date:2020-06-03
Resolution:1.5 Å
 
Kinase:TTBK2
Family:TTBK
Group:CK1
Species:HUMAN
 
Quality Score:6.8
Missing Residues:3
Missing Atoms:0
DFG conformation:in
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (2.9Å)
 
 
ASP rotation (xDFG.81) :343°
PHE rotation (xDFG.82) :
Activation loop position:-3.8Å
αC-helix position:16.7Å
 
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
The following waters were found in the defined clusters:
I1
H-bond protein
I5
H-bond protein
I11
H-bond ligand
Binding pocket sequence
UniprotRKIGGGGFGEIYDVALKVEVLKMEVAVLKKLQDHVCRFIGCYVVMQLQG-RNLADLRRSSIHSVGFLHRDIKPSNFAMMLDFGLA
Structure:RKIGG___GEIYDVALKVEVLKMEVAVLKKLQDHVCRFIGCYVVMQLQG_RNLADLRRSSIHSVGFLHRDIKPSNFAMMLDFGLA


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: ADP
Ligand Name: ADENOSINE-5'-DIPHOSPHATE

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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
25
2 K
26
3 I
27
4 G
28
5 G
29
6 _
_
7 _
_
8 _
_
9 G
33
10 E
34
11 I
35
12 Y
36
13 D
37
14 V
47
15 A
48
16 L
49
17 K
50
18 V
51
19 E
52
20 V
60
αC b.l IV
21 L
61
22 K
62
23 M
63
24 E
64
25 V
65
26 A
66
27 V
67
28 L
68
29 K
69
30 K
70
31 L
71
32 Q
72
33 D
75
34 H
76
35 V
77
36 C
78
37 R
79
38 F
80
39 I
81
40 G
82
IV V GK hinge linker αD αE
41 C
83
42 Y
91
43 V
92
44 V
93
45 M
94
46 Q
95
47 L
96
48 Q
97
49 G
98
50 _
_
51 R
99
52 N
100
53 L
101
54 A
102
55 D
103
56 L
104
57 R
105
58 R
106
59 S
107
60 S
131
αE VI c.l VII VIII x
61 I
132
62 H
133
63 S
134
64 V
135
65 G
136
66 F
137
67 L
138
68 H
139
69 R
140
70 D
141
71 I
142
72 K
143
73 P
144
74 S
145
75 N
146
76 F
147
77 A
148
78 M
149
79 M
161
80 L
162
DFG a.l
81 D
163
82 F
164
83 G
165
84 L
166
85 A
167

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Binding affinities
ChEMBL ID:CHEMBL14830
Bioaffinities: 2 records for 1 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensMitogen-activated protein kinase kinase kinase 74.24.25.4pKd2