Research workbench
Orally active aminopyridines as inhibitors of tetrameric fructose 1,6-bisphosphatase
Analyse Orally active aminopyridines as inhibitors of tetrameric fructose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y5L
- Type
- protein
- Length
- 2,540 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-1,6-bisphosphatase 1
- EC
- 3.1.3.11
- UniProt
- P09467
- Ligands
- RO8
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) | protein | 319 | 39% helix, 24% strand | P09467 |
| B, C, D, F, G, H | Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) | protein | 317 | 39% helix, 26% strand | P09467 |
Ligands and binding sites
- RO8 · N-{[(2Z)-5-bromo-1,3-thiazol-2(3H)-ylidene]carbamoyl}-3-chlorobenzenesulfonamide · ligand · 8 copies · chains A, C, B, D, E, G, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.84 | 0.85 | 114 | empty |
| 2 | 956 | 0.84 | 0.85 | 96 | empty |
| 3 | 557 | 0.74 | 0.82 | 76 | empty |
| 4 | 387 | 0.68 | 0.80 | 45 | RO8 |
| 5 | 386 | 0.67 | 0.80 | 44 | RO8 |
Interfaces
14 interfaces between chains.
- E–F · 2413 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2411 Ų buried · 37 hydrogen bonds · protein-protein
- G–H · 2383 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2376 Ų buried · 29 hydrogen bonds · protein-protein
- F–H · 1321 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2Y5L · orally active aminopyridines as inhibitors of tetrameric fructose 1,6- bisphosphatase · the same entry in another collection · chain H against H, TM-score 1.00
- P09467 · AlphaFold monomer V2.0 prediction for fructose-1,6-bisphosphatase 1 (P09467) · a predicted model of the same protein · chain F against A, TM-score 0.97
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 P09467
- Elsewhere: RCSB PDB 2Y5L · PDBe 2Y5L · UniProt P09467
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