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) : | 0° |
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
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
Uniprot | RKIGGGGFGEIYDVALKVEVLKMEVAVLKKLQDHVCRFIGCYVVMQLQG-RNLADLRRSSIHSVGFLHRDIKPSNFAMMLDFGLA |
Structure: | RKIGG___GEIYDVALKVEVLKMEVAVLKKLQDHVCRFIGCYVVMQLQG_RNLADLRRSSIHSVGFLHRDIKPSNFAMMLDFGLA |
Modified residues
No modified residues identified.
Orthosteric ligand
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- LABELS
- KLIFS residue #
- Amino Acid
- None
- COLORS
- Interaction types
- KLIFS (all res.)
- KLIFS (interacting res.)
- None
- OTHER
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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 | |||||||||||||||
Binding affinities
ChEMBL ID:CHEMBL14830Bioaffinities: 2 records for 1 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Mitogen-activated protein kinase kinase kinase 7 | 4.2 | 4.2 | 5.4 | pKd | 2 |