MolNFT v1 · #92274 · protein
Human PDE9 in complex with selective compound
4G2J · High affinity cgmp-specific 3',5'-cyclic phosphodiesterase…: “Human PDE9 in complex with selective compound”. X-ray diffraction, 3 ligands (0WF, ZN, MG), 4 pockets (best druggability 0.75). MolNFT v1 #92274 on GenesisL1: 3D…
- PDB
- 4G2J
- Type
- protein
- Length
- 656 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
- 0WF, ZN, MG
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 72% 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 | 328 | 72% helix, 0% strand | O76083 |
Ligands and binding sites
- 0WF · 1-cyclopentyl-6-[(1R)-1-(3-phenoxyazetidin-1-yl)ethyl]-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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.75 | 0.85 | 43 | MG, 0WF |
| 2 | 365 | 0.74 | 0.85 | 38 | MG, 0WF |
| 3 | 130 | 0.40 | 0.75 | 24 | empty |
| 4 | 64 | 0.34 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 849 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
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 4G2J · PDBe 4G2J · UniProt O76083
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