MolNFT v1 · #178278 · protein
Crystal structure of PDE5A in complex with inhibitor L12
7FAR · Cgmp-specific 3',5'-cyclic phosphodiesterase: “Crystal structure of PDE5A in complex with inhibitor L12”. X-ray diffraction, 3 ligands (2VI, ZN, MG), 3 pockets (best druggability 0.65). MolNFT v1 #178278 on GenesisL1: 3D structure…
- PDB
- 7FAR
- Type
- protein
- Length
- 292 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
- 2VI, ZN, MG
- Pockets
- 3 · best druggability 0.65
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 | 292 | 69% helix, 0% strand | O76074 |
Ligands and binding sites
- 2VI · 5-[bis(fluoranyl)methoxy]-2-[(4-chlorophenyl)methyl]-10-(3-methoxypropyl)-3,10-diazatricyclo[6.4.1.0^{4, 13}]trideca-1,4(13),5,7-tetraen-9-one · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.65 | 0.80 | 39 | MG, 2VI |
| 2 | 91 | 0.53 | 0.84 | 26 | empty |
| 3 | 69 | 0.43 | 0.81 | 20 | empty |
Compared structures
- 7FAR · Crystal structure of PDE5A in complex with inhibitor L12 · 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 7FAR · PDBe 7FAR · UniProt O76074
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