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Crystal structure of phosphodiesterase 9 in complex with (S)-C33
Analyse Crystal structure of phosphodiesterase 9 in complex with (S)-C33 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y8C
- Type
- protein
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- High affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9A
- EC
- 3.1.4.35
- UniProt
- O76083
- Ligands
- 49D, ZN, MG
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | High affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9A (EC 3.1.4.35) | protein | 322 | 72% helix, 0% strand | O76083 |
| B | High affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9A (EC 3.1.4.35) | protein | 326 | 71% helix, 0% strand | O76083 |
Ligands and binding sites
- 49D · 6-{[(1S)-1-(4-chlorophenyl)ethyl]amino}-1-cyclopentyl-1,5-dihydro-4H-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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.73 | 0.84 | 37 | 49D, MG |
| 2 | 369 | 0.72 | 0.84 | 45 | 49D, MG |
| 3 | 75 | 0.40 | 0.79 | 19 | empty |
| 4 | 53 | 0.37 | 0.80 | 17 | empty |
| 5 | 78 | 0.36 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 886 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4Y8C · Crystal structure of phosphodiesterase 9 in complex with (S)-C33 · the same entry in another collection · chain A against A, TM-score 1.00
- O76083 · AlphaFold monomer V2.0 prediction for high affinity cgmp-specific 3',5'-cyclic… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O76083
- Elsewhere: RCSB PDB 4Y8C · PDBe 4Y8C · UniProt O76083
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