Research workbench
Crystal structure of PDE9 in complex with racemic inhibitor C33
Analyse Crystal structure of PDE9 in complex with racemic inhibitor C33 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y86
- 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, 49E, ZN, MG
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 71% 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 | 70% helix, 0% strand | O76083 |
| B | High affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9A (EC 3.1.4.35) | protein | 326 | 72% 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 · chains A
- 49E · 6-{[(1R)-1-(4-chlorophenyl)ethyl]amino}-1-cyclopentyl-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one · ligand · chains 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.72 | 0.84 | 43 | 49E, MG |
| 2 | 365 | 0.72 | 0.84 | 39 | 49D, MG |
| 3 | 81 | 0.44 | 0.80 | 20 | empty |
| 4 | 79 | 0.42 | 0.79 | 20 | empty |
| 5 | 77 | 0.38 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 852 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4Y86 · Crystal structure of PDE9 in complex with racemic inhibitor C33 · the same entry in another collection · chain B against B, 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 4Y86 · PDBe 4Y86 · UniProt O76083
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