5O26 - chain A (model B) | WNK lysine deficient protein kinase 3
Structure information
PDB: | 5O26 |
PubMed: | - |
Release date: | 2017-06-28 |
Resolution: | 2.38 Å |
Kinase: | WNK3 (Wnk3) |
Family: | WNK |
Group: | Other |
Species: | HUMAN |
Quality Score: | 9.4 |
Missing Residues: | 0 |
Missing Atoms: | 6 |
DFG conformation: | in |
αC-helix conformation: | out |
Salt bridge KIII.17 and EαC.24: | No |
ASP rotation (xDFG.81) : | 347° |
PHE rotation (xDFG.82) : | 355° |
Activation loop position: | -3.2Å |
αC-helix position: | 22.2Å |
G-rich loop angle: | 51.9° |
G-rich loop distance: | 14.5Å |
G-rich loop rotation: | 28.7° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I3
H-bond protein
I5
H-bond protein
I6
H-bond ligand
H-bond protein
I11
H-bond protein
Binding pocket sequence
Uniprot | IELGRGAFKTVYKVAWCELRFKEEAEMLKGLQPNIVRFYDSVLVTELMTSGTLKTYLKRHTRTPPIIHRDLKCDNIFIIGDLGLA |
Structure: | IELGRGAFKTVYKVAWCELRFKEEAEMLKGLQPNIVRFYDSVLVTELMTSGTLKTYLKRHTRTPPIIHRDLKCDNIFIIGDLGLA |
Modified residues
Residue 304 (not in pocket)
Phosphorylated serine
Residue 308 (not in pocket)
Phosphorylated serine
Orthosteric ligand
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- LABELS
- KLIFS residue #
- Amino Acid
- None
- COLORS
- Interaction types
- KLIFS (all res.)
- KLIFS (interacting res.)
- None
- OTHER
- Show/hide non-interacting res.
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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 I 151 | 2 E 152 | 3 L 153 | 4 G 154 | 5 R 155 | 6 G 156 | 7 A 157 | 8 F 158 | 9 K 159 | 10 T 160 | 11 V 161 | 12 Y 162 | 13 K 163 | 14 V 173 | 15 A 174 | 16 W 175 | 17 C 176 | 18 E 177 | 19 L 178 | 20 R 190 |
■ | ■ | ■ | ▲ | ▲ | ■▲ | ■ | ■ | ||||||||||||
αC | b.l | IV | |||||||||||||||||
21 F 191 | 22 K 192 | 23 E 193 | 24 E 194 | 25 A 195 | 26 E 196 | 27 M 197 | 28 L 198 | 29 K 199 | 30 G 200 | 31 L 201 | 32 Q 202 | 33 P 204 | 34 N 205 | 35 I 206 | 36 V 207 | 37 R 208 | 38 F 209 | 39 Y 210 | 40 D 211 |
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 S 212 | 42 V 224 | 43 L 225 | 44 V 226 | 45 T 227 | 46 E 228 | 47 L 229 | 48 M 230 | 49 T 231 | 50 S 232 | 51 G 233 | 52 T 234 | 53 L 235 | 54 K 236 | 55 T 237 | 56 Y 238 | 57 L 239 | 58 K 240 | 59 R 241 | 60 H 265 |
▲ | ■ | ■▲ | |||||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 T 266 | 62 R 267 | 63 T 268 | 64 P 269 | 65 P 270 | 66 I 271 | 67 I 272 | 68 H 273 | 69 R 274 | 70 D 275 | 71 L 276 | 72 K 277 | 73 C 278 | 74 D 279 | 75 N 280 | 76 I 281 | 77 F 282 | 78 I 283 | 79 I 292 | 80 G 293 |
▲ | ▲ | ■♦ | |||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 294 | 82 L 295 | 83 G 296 | 84 L 297 | 85 A 298 | |||||||||||||||
Binding affinities
ChEMBL ID:CHEMBL1230989Bioaffinities: No (p)Ki/(p)IC50/(p)EC50 values for kinases found (with a ChEMBL confidence ≥ 8).