MolNFT v1 · #104628 · protein
Phosphodiesterase-9A in complex with inhibitor wyq-C36D
4QGE · Phosphodiesterase 9A: “Phosphodiesterase-9A in complex with inhibitor wyq-C36D”. X-ray diffraction, 3 ligands (35O, ZN, MG), 5 pockets (best druggability 0.74). MolNFT v1 #104628 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4QGE
- Type
- protein
- Length
- 642 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphodiesterase 9A
- UniProt
- K7AGW3
- Ligands
- 35O, ZN, MG
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphodiesterase 9A | protein | 322 | 72% helix, 0% strand | K7AGW3 |
| B | Phosphodiesterase 9A | protein | 320 | 72% helix, 0% strand | K7AGW3 |
Ligands and binding sites
- 35O · N~2~-(1-cyclopentyl-4-oxo-4,7-dihydro-1H-pyrazolo[3,4-d]pyrimidin-6-yl)-N-(4-methoxyphenyl)-D-alaninamide · 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
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 | 343 | 0.74 | 0.85 | 41 | 35O, MG |
| 2 | 361 | 0.73 | 0.84 | 47 | 35O, MG |
| 3 | 81 | 0.41 | 0.79 | 19 | empty |
| 4 | 72 | 0.34 | 0.76 | 12 | empty |
| 5 | 55 | 0.29 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 839 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4QGE · phosphodiesterase-9A in complex with inhibitor WYQ-C36D · 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 K7AGW3
- Elsewhere: RCSB PDB 4QGE · PDBe 4QGE · UniProt K7AGW3
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