MolNFT v1 · #54462 · protein
Cell-penetrant, nanomolar O-glcnacase inhibitors selective against lysosomal hexosaminidases
2XPK · O-glcnacase nagj: “Cell-penetrant, nanomolar O-glcnacase inhibitors selective against lysosomal hexosaminidases”. X-ray diffraction, 1 ligand (Z0M), 12 pockets (best druggability 0.77). MolNFT v1 #54462 on GenesisL1: 3D structure…
- PDB
- 2XPK
- Type
- protein
- Length
- 1,170 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-glcnacase nagj
- EC
- 3.2.1.52
- UniProt
- Q0TR53
- Ligands
- Z0M
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | O-glcnacase nagj (EC 3.2.1.52) | protein | 585 | 46% helix, 15% strand | Q0TR53 |
Ligands and binding sites
- Z0M · N-[(5R,6R,7R,8S)-6,7-dihydroxy-5-(hydroxymethyl)-2-(2-phenylethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridin-8-yl]-3-sulfanylpropanamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.77 | 0.79 | 81 | empty |
| 2 | 502 | 0.75 | 0.83 | 59 | Z0M |
| 3 | 521 | 0.72 | 0.81 | 65 | Z0M |
| 4 | 153 | 0.49 | 0.78 | 28 | empty |
| 5 | 129 | 0.47 | 0.78 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1209 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2XPK · Cell-penetrant, nanomolar O-GlcNAcase inhibitors selective against lysosomal… · the same entry in another collection · chain A against A, TM-score 1.00
- Q0TR53 · AlphaFold monomer V2.0 prediction for O-glcnacase nagj (Q0TR53) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q0TR53
- Elsewhere: RCSB PDB 2XPK · PDBe 2XPK · UniProt Q0TR53
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