5TF9 - chain A | WNK lysine deficient protein kinase 1
Structure information
PDB: | 5TF9 |
PubMed: | 27712055 |
Release date: | 2016-10-19 |
Resolution: | 2.5 Å |
Kinase: | WNK1 (Wnk1) |
Family: | WNK |
Group: | Other |
Species: | HUMAN |
Quality Score: | 8 |
Missing Residues: | 0 |
Missing Atoms: | 0 |
DFG conformation: | in |
αC-helix conformation: | out |
Salt bridge KIII.17 and EαC.24: | No |
ASP rotation (xDFG.81) : | 357° |
PHE rotation (xDFG.82) : | 10° |
Activation loop position: | -3.8Å |
αC-helix position: | 22.1Å |
G-rich loop angle: | 57.9° |
G-rich loop distance: | 16.7Å |
G-rich loop rotation: | 40.1° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond ligand
H-bond protein
I11
H-bond ligand
Binding pocket sequence
Uniprot | IEIGRGSFKTVYKVAWCELRFKEEAEMLKGLQPNIVRFYDSVLVTELMTSGTLKTYLKRHTRTPPIIHRDLKCDNIFIIGDLGLA |
Structure: | IEIGRGSFKTVYKVAWCELRFKEEAEMLKGLQPNIVRFYDSVLVTELMTSGTLKTYLKRHTRTPPIIHRDLKCDNIFIIGDLGLA |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: 7AV
Ligand Name: {2-[(4-chlorophenyl)methoxy]phenyl}{5-[2-(methylamino)-1,3-thiazol-4-yl]-2,3-dihydro-1H-indol-1-yl}methanone
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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.
- En/disable resizing interacting res.
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 225 | 2 E 226 | 3 I 227 | 4 G 228 | 5 R 229 | 6 G 230 | 7 S 231 | 8 F 232 | 9 K 233 | 10 T 234 | 11 V 235 | 12 Y 236 | 13 K 237 | 14 V 247 | 15 A 248 | 16 W 249 | 17 C 250 | 18 E 251 | 19 L 252 | 20 R 264 |
■ | ■ | ▲ | ▲ | ■ | ■ | ■ | |||||||||||||
αC | b.l | IV | |||||||||||||||||
21 F 265 | 22 K 266 | 23 E 267 | 24 E 268 | 25 A 269 | 26 E 270 | 27 M 271 | 28 L 272 | 29 K 273 | 30 G 274 | 31 L 275 | 32 Q 276 | 33 P 278 | 34 N 279 | 35 I 280 | 36 V 281 | 37 R 282 | 38 F 283 | 39 Y 284 | 40 D 285 |
■♦ | ■ | ■ | ■ | ■ | ■ | ■ | ■▲ | ■♦ | |||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 S 286 | 42 V 298 | 43 L 299 | 44 V 300 | 45 T 301 | 46 E 302 | 47 L 303 | 48 M 304 | 49 T 305 | 50 S 306 | 51 G 307 | 52 T 308 | 53 L 309 | 54 K 310 | 55 T 311 | 56 Y 312 | 57 L 313 | 58 K 314 | 59 R 315 | 60 H 339 |
■ | ■ | ▲ | ■ | ■▲ | ■ | ||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 T 340 | 62 R 341 | 63 T 342 | 64 P 343 | 65 P 344 | 66 I 345 | 67 I 346 | 68 H 347 | 69 R 348 | 70 D 349 | 71 L 350 | 72 K 351 | 73 C 352 | 74 D 353 | 75 N 354 | 76 I 355 | 77 F 356 | 78 I 357 | 79 I 366 | 80 G 367 |
■ | ▲ | ■♦ | ■ | ||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 368 | 82 L 369 | 83 G 370 | 84 L 371 | 85 A 372 | |||||||||||||||
■ | ■ | ■ | ■ |
Binding affinities
ChEMBL ID:CHEMBL4100485Bioaffinities: 1 record for 1 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Serine/threonine-protein kinase WNK1 | 6.4 | 6.4 | 6.4 | pIC50 | 1 |