MolNFT v1 · #136570 · protein
Crystal structure of rat cathepsin D with (5S)-3-(5,6-dihydro-2H- pyran-3-yl)-1-fluoro- 7-(2-fluoropyridin-3-YL)SPIRO[CHROMENO[2,3- C]PYRIDINE-5,4'-[1,3]OXAZOL]-2'-amine
5UX4: “Crystal structure of rat cathepsin D with (5S)-3-(5,6-dihydro-2H- pyran-3-yl)-1-fluoro…”. X-ray diffraction, 2 ligands (3UT, NAG), 4 pockets (best druggability 0.75). MolNFT v1 #136570 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5UX4
- Type
- protein
- Length
- 677 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin D
- EC
- 3.4.23.5
- UniProt
- P24268
- Ligands
- 3UT, NAG
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin D (EC 3.4.23.5) | protein | 337 | 13% helix, 45% strand | P24268 |
| B | Cathepsin D (EC 3.4.23.5) | protein | 340 | 15% helix, 45% strand | P24268 |
Ligands and binding sites
- 3UT · (5S)-3-(5,6-dihydro-2H-pyran-3-yl)-1-fluoro-7-(2-fluoropyridin-3-yl)spiro[chromeno[2,3-c]pyridine-5,4'-[1,3]oxazol]-2'-amine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.75 | 0.82 | 47 | 3UT |
| 2 | 706 | 0.74 | 0.79 | 74 | 3UT |
| 3 | 251 | 0.55 | 0.77 | 35 | empty |
| 4 | 247 | 0.51 | 0.75 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 396 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5UX4 · Crystal Structure of Rat Cathepsin D with (5S)-3-(5,6-dihydro-2H-pyran-3-yl)-1-fluoro… · the same entry in another collection · chain A against A, TM-score 1.00
- P24268 · AlphaFold monomer V2.0 prediction for cathepsin D (P24268) · a predicted model of the same protein · chain B 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 P24268
- Elsewhere: RCSB PDB 5UX4 · PDBe 5UX4 · UniProt P24268
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