Research workbench
PDE2 catalytic domain complexed with inhibitors
Analyse PDE2 catalytic domain complexed with inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U7L
- Type
- protein
- Length
- 987 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-dependent 3',5'-cyclic phosphodiesterase
- EC
- 3.1.4.17
- UniProt
- O00408
- Ligands
- 7Y4, ZN, MG
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 339 | 70% helix, 0% strand | O00408 |
| B | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 310 | 70% helix, 0% strand | O00408 |
| C | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 338 | 67% helix, 0% strand | O00408 |
Ligands and binding sites
- 7Y4 · (3R)-1-{3-[5-(4-ethylphenyl)-1-methyl-1H-pyrazol-4-yl]-1-methyl-1H-pyrazolo[3,4-d]pyrimidin-4-yl}-N,N-dimethylpyrrolidin-3-amine · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.76 | 0.85 | 42 | 7Y4, MG |
| 2 | 1092 | 0.76 | 0.78 | 91 | empty |
| 3 | 464 | 0.76 | 0.84 | 40 | 7Y4, MG |
| 4 | 475 | 0.74 | 0.83 | 40 | 7Y4, MG |
| 5 | 82 | 0.65 | 0.91 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 813 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 177 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 66 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5U7L · PDE2 catalytic domain complexed with inhibitors · 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 O00408
- Elsewhere: RCSB PDB 5U7L · PDBe 5U7L · UniProt O00408
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.