Research workbench
PDE2A catalytic domain in complex with a brain penetrant inhibitor
Analyse PDE2A catalytic domain in complex with a brain penetrant inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D09
- Type
- protein
- Length
- 1,333 residues
- Chains
- 4
- 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
- 788, ZN, MG
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 4 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 | 340 | 69% helix, 0% strand | O00408 |
| B | Cgmp-dependent 3', 5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 338 | 69% helix, 0% strand | O00408 |
| C | Cgmp-dependent 3', 5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 329 | 70% helix, 0% strand | O00408 |
| D | Cgmp-dependent 3', 5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 326 | 69% helix, 0% strand | O00408 |
Ligands and binding sites
- 788 · N-benzyl-4-methyl-1-phenyl[1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.73 | 0.85 | 36 | 788, MG |
| 2 | 338 | 0.73 | 0.85 | 41 | 788, MG |
| 3 | 583 | 0.72 | 0.80 | 67 | empty |
| 4 | 365 | 0.71 | 0.83 | 36 | 788, MG |
| 5 | 325 | 0.71 | 0.84 | 38 | 788, MG |
Interfaces
6 interfaces between chains.
- A–B · 728 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 386 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 343 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 197 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 104 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4D09 · PDE2a catalytic domain in complex with a brain penetrant inhibitor · 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 4D09 · PDBe 4D09 · UniProt O00408
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