Research workbench
[1,2,4]TRIAZOLO[1,5-A]PYRIMIDINE phosphodiesterase 2 inhibitors
Analyse [1,2,4]TRIAZOLO[1,5-A]PYRIMIDINE phosphodiesterase 2 inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZND
- Type
- protein
- Length
- 658 residues
- Chains
- 2
- 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
- QMZ, ZN, MG
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 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 | 324 | 67% helix, 0% strand | O00408 |
| B | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 334 | 70% helix, 0% strand | O00408 |
Ligands and binding sites
- QMZ · [(3~{S})-3-([1,2,4]triazolo[1,5-a]pyrimidin-7-yl) piperidin-1-yl]-(3,4,5-trimethoxyphenyl)methanone · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 765 | 0.84 | 0.88 | 67 | MG, QMZ |
| 2 | 350 | 0.71 | 0.83 | 36 | MG, QMZ |
| 3 | 177 | 0.53 | 0.79 | 34 | empty |
| 4 | 114 | 0.51 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 841 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6ZND · [1,2,4]Triazolo[1,5-a]pyrimidine Phosphodiesterase 2 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 6ZND · PDBe 6ZND · UniProt O00408
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