3WF6 - chain A (model B) | Ribosomal protein S6 kinase B1
Structure information
PDB: | 3WF6 |
PubMed: | 25078151 |
Release date: | 2014-08-06 |
Resolution: | 2.03 Å |
Kinase: | RPS6KB1 (p70S6K) |
Family: | RSK |
Group: | AGC |
Species: | HUMAN |
Quality Score: | 9.4 |
Missing Residues: | 1 |
Missing Atoms: | 2 |
DFG conformation: | in |
αC-helix conformation: | in |
Salt bridge KIII.17 and EαC.24: | Yes (2.7Å) |
ASP rotation (xDFG.81) : | 341° |
PHE rotation (xDFG.82) : | 20° |
Activation loop position: | -3.3Å |
αC-helix position: | 17.5Å |
G-rich loop angle: | 58.2° |
G-rich loop distance: | 18.5Å |
G-rich loop rotation: | 43.7° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I7
H-bond ligand
Binding pocket sequence
Uniprot | RVLGKGGYGKVFQFAMKVLHTKAERNILEEVKPFIVDLIYAYLILEYLSGGELFMQLERHLHQKGIIYRDLKPENIMLLTDFGLC |
Structure: | RVLGKGGYGKVFQFAMKVL_TKAERNILEEVKPFIVDLIYAYLILEYLSGGELFMQLERHLHQKGIIYRDLKPENIMLLTDFGLC |
Modified residues
Residue 252 (not in pocket)
Phosphorylated threonine
Orthosteric ligand
Ligand HET-code: FZ9
Ligand Name: 4-[4-(1H-indol-3-yl)-3,6-dihydropyridin-1(2H)-yl]-1H-pyrazolo[3,4-d]pyrimidine
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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 95 | 2 V 96 | 3 L 97 | 4 G 98 | 5 K 99 | 6 G 100 | 7 G 101 | 8 Y 102 | 9 G 103 | 10 K 104 | 11 V 105 | 12 F 106 | 13 Q 107 | 14 F 120 | 15 A 121 | 16 M 122 | 17 K 123 | 18 V 124 | 19 L 125 | 20 _ _ |
■ | ■ | ■ | ■ | ■ | ■ | ■ | ■ | ||||||||||||
αC | b.l | IV | |||||||||||||||||
21 T 140 | 22 K 141 | 23 A 142 | 24 E 143 | 25 R 144 | 26 N 145 | 27 I 146 | 28 L 147 | 29 E 148 | 30 E 149 | 31 V 150 | 32 K 151 | 33 P 153 | 34 F 154 | 35 I 155 | 36 V 156 | 37 D 157 | 38 L 158 | 39 I 159 | 40 Y 160 |
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 A 161 | 42 Y 169 | 43 L 170 | 44 I 171 | 45 L 172 | 46 E 173 | 47 Y 174 | 48 L 175 | 49 S 176 | 50 G 177 | 51 G 178 | 52 E 179 | 53 L 180 | 54 F 181 | 55 M 182 | 56 Q 183 | 57 L 184 | 58 E 185 | 59 R 186 | 60 H 208 |
■ | ▲ | ■♦ | ■▲ | ||||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 L 209 | 62 H 210 | 63 Q 211 | 64 K 212 | 65 G 213 | 66 I 214 | 67 I 215 | 68 Y 216 | 69 R 217 | 70 D 218 | 71 L 219 | 72 K 220 | 73 P 221 | 74 E 222 | 75 N 223 | 76 I 224 | 77 M 225 | 78 L 226 | 79 L 234 | 80 T 235 |
■ | ■ | ||||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 236 | 82 F 237 | 83 G 238 | 84 L 239 | 85 C 240 | |||||||||||||||
Binding affinities
Ligand not found in ChEMBL.