MolNFT v1 · #38624 · protein
Crystal structure of PDE5 in complex with sildenafil
2H42 · Cgmp-specific 3',5'-cyclic phosphodiesterase: “Crystal structure of PDE5 in complex with sildenafil”. X-ray diffraction, 3 ligands (VIA, ZN, MG), 14 pockets (best druggability 0.83). MolNFT v1 #38624 on GenesisL1: 3D structure…
- PDB
- 2H42
- Type
- protein
- Length
- 960 residues
- Chains
- 3
- 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
- VIA, ZN, MG
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.35) | protein | 326 | 70% helix, 0% strand | O76074 |
| B, C | Cgmp-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.35) | protein | 317 | 70% helix, 0% strand | O76074 |
Ligands and binding sites
- VIA · 5-{2-ethoxy-5-[(4-methylpiperazin-1-yl)sulfonyl]phenyl}-1-methyl-3-propyl-1H,6H,7H-pyrazolo[4,3-d]pyrimidin-7-one · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 769 | 0.83 | 0.86 | 72 | MG, VIA |
| 2 | 477 | 0.81 | 0.88 | 47 | MG, VIA |
| 3 | 501 | 0.77 | 0.85 | 49 | VIA |
| 4 | 201 | 0.66 | 0.85 | 36 | empty |
| 5 | 243 | 0.66 | 0.83 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 788 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 500 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 443 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2H42 · Crystal structure of PDE5 in complex with sildenafil · the same entry in another collection · chain A against A, TM-score 1.00
- O76074 · AlphaFold monomer V2.0 prediction for cgmp-specific 3',5'-cyclic phosphodiesterase… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 2H42 · PDBe 2H42 · UniProt O76074
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.