MolNFT v1 · #165706 · protein
PCSK9 in complex with compound 2
6U3X · Proprotein convertase SUBTILISIN/KEXIN type 9: “PCSK9 in complex with compound 2”. X-ray diffraction, 1 ligand (PVV), 5 pockets (best druggability 0.75). MolNFT v1 #165706 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6U3X
- Type
- protein
- Length
- 578 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
- PVV
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 37% 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 | 486 | 17% helix, 37% strand | Q8NBP7 |
Ligands and binding sites
- PVV · 2-[(1R)-6,7-dimethoxy-1-methyl-1,2,3,4-tetrahydroisoquinolin-1-yl]-N-(1,3-thiazol-2-yl) acetamide · 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 | 699 | 0.75 | 0.80 | 87 | PVV |
| 2 | 299 | 0.70 | 0.84 | 41 | empty |
| 3 | 169 | 0.46 | 0.75 | 31 | empty |
| 4 | 116 | 0.41 | 0.76 | 34 | empty |
| 5 | 58 | 0.29 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1390 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6U3X · PCSK9 in complex with compound 2 · 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 6U3X · PDBe 6U3X · UniProt Q8NBP7
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