Research workbench
Selective inhibitors of PDE2, PDE9, and PDE10: modulators of activity of the central nervous system
Analyse Selective inhibitors of PDE2, PDE9, and PDE10: modulators of activity of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C1I
- Type
- protein
- Length
- 1,283 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
- EH9, ZN, MG
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-dependent 3', 5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 325 | 70% helix, 0% strand | O00408 |
| B | Cgmp-dependent 3', 5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 320 | 71% helix, 0% strand | O00408 |
| C, D | Cgmp-dependent 3', 5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 319 | 71% helix, 0% strand | O00408 |
Ligands and binding sites
- EH9 · (2S,3R)-3-(6-amino-9H-purin-9-yl)nonan-2-ol · 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
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.77 | 0.85 | 40 | EH9, MG |
| 2 | 461 | 0.77 | 0.85 | 41 | EH9, MG |
| 3 | 433 | 0.76 | 0.85 | 42 | EH9, MG |
| 4 | 423 | 0.75 | 0.84 | 38 | EH9, MG |
| 5 | 231 | 0.60 | 0.80 | 40 | empty |
Interfaces
3 interfaces between chains.
- A–B · 638 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 434 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 47 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4C1I · Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Activity of the Central… · 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 4C1I · PDBe 4C1I · UniProt O00408
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