Research workbench
PCSK9 in complex with compound 16
Analyse PCSK9 in complex with compound 16 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U26
- Type
- protein
- Length
- 571 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proprotein convertase SUBTILISIN/KEXIN type 9
- EC
- 3.4.21.-
- UniProt
- Q8NBP7
- Ligands
- 063
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 92 | 30% helix, 39% strand | Q8NBP7 |
| B | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 479 | 17% helix, 38% strand | Q8NBP7 |
Ligands and binding sites
- 063 · 4'-{[(1R)-6-{2-[2-({N~5~-[N,N'-bis(tert-butoxycarbonyl)carbamimidoyl]-N~2~-(tert-butoxycarbonyl)-L-ornithyl}amino)ethoxy]ethoxy}-1-methyl-1-{2-oxo-2-[(1,3-thiazol-2-yl)amino]ethyl}-1,2, 3,4-tetrahydroisoquinolin-7-yl]oxy}-2'-fluoro[1,1'-biphenyl]-4-carboxylic acid · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 648 | 0.74 | 0.81 | 82 | 063 |
| 2 | 312 | 0.66 | 0.82 | 46 | empty |
| 3 | 139 | 0.43 | 0.75 | 25 | empty |
| 4 | 57 | 0.28 | 0.74 | 13 | empty |
| 5 | 58 | 0.25 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1419 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6U26 · PCSK9 in complex with compound 16 · the same entry in another collection · chain A against A, 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 Q8NBP7
- Elsewhere: RCSB PDB 6U26 · PDBe 6U26 · UniProt Q8NBP7
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