MolNFT v1 · #90096 · protein
Human phosphodiesterase 9 in complex with inhibitors
4E90 · High affinity cgmp-specific 3',5'-cyclic phosphodiesterase…: “Human phosphodiesterase 9 in complex with inhibitors”. X-ray diffraction, 3 ligands (7RG, ZN, MG), 4 pockets (best druggability 0.73). MolNFT v1 #90096 on GenesisL1: 3D…
- PDB
- 4E90
- 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
- 7RG, ZN, MG
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 71% 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 | 71% helix, 0% strand | O76083 |
Ligands and binding sites
- 7RG · 6-[(3S,4S)-4-methyl-1-(pyrimidin-2-ylmethyl)pyrrolidin-3-yl]-1-(tetrahydro-2H-pyran-4-yl)-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 | 374 | 0.73 | 0.84 | 40 | MG, 7RG |
| 2 | 384 | 0.73 | 0.83 | 36 | MG, 7RG |
| 3 | 94 | 0.41 | 0.78 | 21 | empty |
| 4 | 99 | 0.37 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 864 Ų buried · 11 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 4E90 · PDBe 4E90 · UniProt O76083
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