MolNFT v1 · #165668 · protein
PCSK9 in complex with compound 5
6U2P · Proprotein convertase SUBTILISIN/KEXIN type 9: “PCSK9 in complex with compound 5”. X-ray diffraction, 1 ligand (PUV), 6 pockets (best druggability 0.74). MolNFT v1 #165668 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6U2P
- Type
- protein
- Length
- 573 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
- PUV
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 92 | 28% helix, 39% strand | Q8NBP7 |
| B | Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-) | protein | 481 | 17% helix, 40% strand | Q8NBP7 |
Ligands and binding sites
- PUV · 2-fluoro-4-{[(1R)-6-methoxy-1-methyl-1-{2-oxo-2-[(1,3-thiazol-2-yl)amino]ethyl}-1,2,3,4-tetrahydroisoquinolin-7-yl]oxy}benzoic acid · ligand · chains B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.74 | 0.82 | 63 | PUV |
| 2 | 324 | 0.73 | 0.85 | 49 | empty |
| 3 | 58 | 0.37 | 0.80 | 17 | empty |
| 4 | 97 | 0.36 | 0.74 | 19 | empty |
| 5 | 56 | 0.33 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1410 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6U2P · PCSK9 in complex with compound 5 · 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 6U2P · PDBe 6U2P · UniProt Q8NBP7
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