Research workbench
PDE2 in complex with compound 1
Analyse PDE2 in complex with compound 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B98
- Type
- protein
- Length
- 693 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
- D07, ZN, MG
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 344 | 66% helix, 0% strand | O00408 |
| B | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 349 | 66% helix, 0% strand | O00408 |
Ligands and binding sites
- D07 · 6-chloro-N,1-dimethyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine · 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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.77 | 0.79 | 101 | empty |
| 2 | 420 | 0.75 | 0.84 | 41 | MG, D07 |
| 3 | 371 | 0.73 | 0.84 | 37 | MG, D07 |
Interfaces
1 interface between chains.
- A–B · 837 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6B98 · PDE2 in complex with compound 1 · 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 6B98 · PDBe 6B98 · UniProt O00408
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