Research workbench
Structure of human TRPA1 in complex with inhibitor gdc-0334
Analyse Structure of human TRPA1 in complex with inhibitor gdc-0334 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WJ5
- Type
- protein
- Length
- 2,248 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily a member 1
- UniProt
- O75762
- Ligands
- LXY
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 65% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily a member 1 | protein | 562 | 65% helix, 3% strand | O75762 |
Ligands and binding sites
- LXY · (4R,5S)-4-fluoro-1-[(4-fluorophenyl)sulfonyl]-5-methyl-N-({5-(trifluoromethyl)-2-[2-(trifluoromethyl) pyrimidin-5-yl]pyridin-4-yl}methyl)-L-prolinamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.86 | 0.94 | 35 | empty |
| 2 | 456 | 0.73 | 0.82 | 52 | LXY |
| 3 | 57 | 0.72 | 0.98 | 12 | empty |
| 4 | 189 | 0.72 | 0.88 | 24 | LXY |
| 5 | 307 | 0.71 | 0.84 | 36 | LXY |
Interfaces
6 interfaces between chains.
- A–B · 3633 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 3592 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 3545 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 3529 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 490 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6WJ5 · Structure of human TRPA1 in complex with inhibitor GDC-0334 · the same entry in another collection · chain A against A, TM-score 1.00
- O75762 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.86
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 O75762
- Elsewhere: RCSB PDB 6WJ5 · PDBe 6WJ5 · UniProt O75762
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