MolNFT v1 · #92718 · protein
Crystal structure of the PDE9A catalytic domain in complex with inhibitor 28
4GH6 · High affinity cgmp-specific 3',5'-cyclic phosphodiesterase…: “Crystal structure of the PDE9A catalytic domain in complex with inhibitor 28”. X-ray diffraction, 3 ligands (LUO, ZN, MG), 4 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 4GH6
- Type
- protein
- Length
- 652 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
- LUO, ZN, MG
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | High affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9A (EC 3.1.4.35) | protein | 326 | 69% helix, 0% strand | O76083 |
Ligands and binding sites
- LUO · N-(4-methoxyphenyl)-N~2~-[1-(2-methylphenyl)-4-oxo-4,5-dihydro-1H-pyrazolo[3,4-d]pyrimidin-6-yl]-L-alaninamide · ligand · 3 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 | 369 | 0.74 | 0.84 | 39 | LUO, MG |
| 2 | 380 | 0.71 | 0.83 | 44 | LUO, MG |
| 3 | 95 | 0.58 | 0.86 | 14 | empty |
| 4 | 206 | 0.50 | 0.76 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1042 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4GH6 · Crystal structure of the PDE9A catalytic domain in complex with inhibitor 28 · 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 A against A, TM-score 0.98
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 4GH6 · PDBe 4GH6 · UniProt O76083
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