Research workbench
Crystal structure of WNK1 in complex with 1-cyclohexyl-N-({6-fluoro-1- [2-(3-METHOXYPHENYL)PYRIDIN-4-yl]-1H-indol-3-YL}METHYL)METHANAMINE (compound 6)
Analyse Crystal structure of WNK1 in complex with 1-cyclohexyl-N-({6-fluoro-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WDY
- Type
- protein
- Length
- 519 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase WNK1
- EC
- 2.7.11.1
- UniProt
- Q9H4A3
- Ligands
- ANP, A6S, MN
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase WNK1 (EC 2.7.11.1) | protein | 260 | 37% helix, 20% strand | Q9H4A3 |
| B | SERINE/THREONINE-protein kinase WNK1 (EC 2.7.11.1) | protein | 259 | 34% helix, 22% strand | Q9H4A3 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- A6S · 1-cyclohexyl-N-({6-fluoro-1-[2-(3-methoxyphenyl) pyridin-4-yl]-1H-indol-3-yl}methyl)methanamine · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.72 | 0.79 | 52 | ANP, A6S, MN |
| 2 | 639 | 0.71 | 0.78 | 55 | MN, ANP, A6S |
| 3 | 59 | 0.58 | 0.90 | 16 | empty |
| 4 | 173 | 0.53 | 0.79 | 20 | empty |
| 5 | 68 | 0.40 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1796 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5WDY · Crystal structure of WNK1 in complex with 1-cyclohexyl-N-({6-fluoro-1-[2-(3-methoxyphenyl)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H4A3 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase WNK1 (Q9H4A3) · a predicted model of the same protein · chain A against A, TM-score 0.92
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9H4A3
- Elsewhere: RCSB PDB 5WDY · PDBe 5WDY · UniProt Q9H4A3
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