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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
- 4D08
- Type
- protein
- Length
- 1,338 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
- Q2T, ZN, MG
- Pockets
- 11 · best druggability 0.77
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 | 339 | 69% helix, 0% strand | O00408 |
| B | Cgmp-dependent 3', 5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 337 | 69% helix, 0% strand | O00408 |
| C | Cgmp-dependent 3', 5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 327 | 68% helix, 0% strand | O00408 |
| D | Cgmp-dependent 3', 5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 335 | 69% helix, 0% strand | O00408 |
Ligands and binding sites
- Q2T · 1-(5-butoxypyridin-3-yl)-4-methyl-8-(morpholin-4-ylmethyl)[1,2,4]triazolo[4,3-a]quinoxaline · 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
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.77 | 0.85 | 42 | Q2T, MG |
| 2 | 439 | 0.76 | 0.85 | 41 | Q2T, MG |
| 3 | 432 | 0.76 | 0.85 | 40 | Q2T, MG |
| 4 | 410 | 0.75 | 0.85 | 39 | Q2T, MG |
| 5 | 1087 | 0.75 | 0.77 | 95 | empty |
Interfaces
6 interfaces between chains.
- A–B · 651 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 367 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 293 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 173 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 93 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4D08 · 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 4D08 · PDBe 4D08 · UniProt O00408
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