MolNFT v1 · #110765 · protein
Complex structure of presenilin homologue psh bound to an inhibitor
4Y6K · Uncharacterized protein psh: “Complex structure of presenilin homologue psh bound to an inhibitor”. X-ray diffraction, 1 ligand (4B5), 9 pockets (best druggability 0.79). MolNFT v1 #110765 on GenesisL1: 3D structure, binding sites…
- PDB
- 4Y6K
- Type
- protein
- Length
- 966 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein psh
- UniProt
- A3CWV0
- Ligands
- 4B5
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein psh | protein | 246 | 75% helix, 0% strand | A3CWV0 |
| B | Uncharacterized protein psh | protein | 245 | 77% helix, 0% strand | A3CWV0 |
| C | Uncharacterized protein psh | protein | 238 | 79% helix, 0% strand | A3CWV0 |
| D | Uncharacterized protein psh | protein | 237 | 78% helix, 0% strand | A3CWV0 |
Ligands and binding sites
- 4B5 · N-{(2R,4S,5S)-2-benzyl-5-[(tert-butoxycarbonyl)amino]-4-hydroxy-6-phenylhexanoyl}-L-leucyl-L-phenylalaninamide · ligand · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.79 | 0.81 | 67 | empty |
| 2 | 907 | 0.76 | 0.78 | 68 | 4B5 |
| 3 | 1053 | 0.74 | 0.77 | 92 | empty |
| 4 | 740 | 0.71 | 0.76 | 60 | 4B5 |
| 5 | 71 | 0.68 | 0.94 | 14 | empty |
Interfaces
2 interfaces between chains.
- C–D · 1012 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 869 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4Y6K · Complex structure of presenilin homologue PSH bound to an inhibitor · the same entry in another collection · chain C against C, TM-score 1.00
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 A3CWV0
- Elsewhere: RCSB PDB 4Y6K · PDBe 4Y6K · UniProt A3CWV0
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