MolNFT v1 · #167127 · protein
Crystal structure of PDE5 in complex with a non-competitive inhibitor
6VBI · Cgmp-specific 3',5'-cyclic phosphodiesterase: “Crystal structure of PDE5 in complex with a non-competitive inhibitor”. X-ray diffraction, 1 ligand (FZA), 5 pockets (best druggability 0.83). MolNFT v1 #167127 on GenesisL1: 3D…
- PDB
- 6VBI
- Type
- protein
- Length
- 605 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-specific 3',5'-cyclic phosphodiesterase
- EC
- 3.1.4.35
- UniProt
- O76074
- Ligands
- FZA
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.35) | protein | 304 | 65% helix, 0% strand | O76074 |
| B | Cgmp-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.35) | protein | 301 | 66% helix, 0% strand | O76074 |
Ligands and binding sites
- FZA · (13bS)-4,9-dimethoxy-14-methyl-8,13,13b,14-tetrahydroindolo[2',3':3,4]pyrido[2,1-b]quinazolin-5(7H)-one · ligand · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 795 | 0.83 | 0.86 | 97 | FZA |
| 2 | 256 | 0.77 | 0.90 | 39 | FZA |
| 3 | 72 | 0.58 | 0.89 | 19 | empty |
| 4 | 115 | 0.40 | 0.75 | 16 | empty |
| 5 | 125 | 0.38 | 0.73 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1189 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6VBI · crystal structure of PDE5 in complex with a non-competitive inhibitor · 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 O76074
- Elsewhere: RCSB PDB 6VBI · PDBe 6VBI · UniProt O76074
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.