MolNFT v1 · #142265 · protein
Crystal structure of PDE5 in complex with inhibitor LW1634
5ZZ2 · Cgmp-specific 3',5'-cyclic phosphodiesterase: “Crystal structure of PDE5 in complex with inhibitor LW1634”. X-ray diffraction, 4 ligands (9M0, ZN, MG), 2 pockets (best druggability 0.66). MolNFT v1 #142265 on GenesisL1: 3D…
- PDB
- 5ZZ2
- Type
- protein
- Length
- 299 residues
- Chains
- 1
- 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
- 9M0, ZN, MG, SO4
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.35) | protein | 299 | 69% helix, 0% strand | O76074 |
Ligands and binding sites
- 9M0 · 3-[(2H-1,3-benzodioxol-5-yl)methyl]-8-fluoro-1-(1,3-thiazol-2-yl)[1]benzopyrano[2,3-c]pyrrol-9(2H)-one · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.66 | 0.80 | 31 | MG, SO4, 9M0 |
| 2 | 112 | 0.51 | 0.82 | 27 | empty |
Compared structures
- 5ZZ2 · Crystal structure of PDE5 in complex with inhibitor LW1634 · 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 A 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 5ZZ2 · PDBe 5ZZ2 · UniProt O76074
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