Research workbench
Phosphodiesterase-9A in complex with inhibitor 4B
Analyse Phosphodiesterase-9A in complex with inhibitor 4B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F0I
- Type
- protein
- Length
- 630 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform PDE9A2 of high affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9A
- EC
- 3.1.4.35
- Ligands
- 06A, ZN, MG
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform PDE9A2 of high affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9A (EC 3.1.4.35) | protein | 316 | 72% helix, 0% strand | — |
| B | Isoform PDE9A2 of high affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9A (EC 3.1.4.35) | protein | 314 | 70% helix, 0% strand | — |
Ligands and binding sites
- 06A · 1-cyclopentyl-6-[[(2R)-1-(6-fluoranyl-2-azaspiro[3.3]heptan-2-yl)-1-oxidanylidene-propan-2-yl]amino]-5H-pyrazolo[3,4-d]pyrimidin-4-one · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.72 | 0.84 | 40 | MG, 06A |
| 2 | 310 | 0.70 | 0.84 | 33 | MG, 06A |
| 3 | 217 | 0.53 | 0.77 | 37 | empty |
| 4 | 131 | 0.46 | 0.77 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 850 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7F0I · phosphodiesterase-9A in complex with inhibitor 4b · 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
- Elsewhere: RCSB PDB 7F0I · PDBe 7F0I
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