Research workbench
Crystal structure of NLRP3 nacht domain in complex with a potent inhibitor
Analyse Crystal structure of NLRP3 nacht domain in complex with a potent inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ALV
- Type
- protein
- Length
- 472 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nacht, lrr and pyd domains-containing protein 3
- UniProt
- Q96P20
- Ligands
- RM5, ADP
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nacht, lrr and pyd domains-containing protein 3 | protein | 472 | 50% helix, 11% strand | Q96P20 |
Ligands and binding sites
- RM5 · 1-[4-chloranyl-2,6-di(propan-2-yl)phenyl]-3-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-urea · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.77 | 0.81 | 66 | ADP |
| 2 | 87 | 0.76 | 0.98 | 20 | empty |
| 3 | 422 | 0.74 | 0.83 | 44 | RM5 |
| 4 | 57 | 0.48 | 0.85 | 18 | empty |
| 5 | 50 | 0.39 | 0.81 | 13 | empty |
Compared structures
- 7ALV · Crystal Structure of NLRP3 NACHT domain in complex with a potent inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q96P20 · AlphaFold monomer V2.0 prediction for nacht, lrr and pyd domains- containing protein 3… · a predicted model of the same protein · chain A against A, TM-score 0.64
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 Q96P20
- Elsewhere: RCSB PDB 7ALV · PDBe 7ALV · UniProt Q96P20
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