Research workbench
Crystal structure of PDE10A in complex with a benzimidazole inhibitor
Analyse Crystal structure of PDE10A in complex with a benzimidazole inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WS8
- Type
- protein
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Homo sapiens
- Molecule
- cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
- EC
- 3.1.4.17, 3.1.4.35
- UniProt
- Q9Y233
- Ligands
- X4C, ZN, MG
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.6 · 1 distinct chain · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A (EC 3.1.4.17, 3.1.4.35) | protein | 324 | 68% helix, 0% strand | Q9Y233 |
Ligands and binding sites
- X4C · 8-methyl-6-[2-(5-methyl-1-phenyl-1H-benzimidazol-2-yl)ethyl]imidazo[1,5-a]pyrimidine · 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 624 | 0.74 | 0.81 | 59 | MG, X4C |
| 2 | 763 | 0.73 | 0.78 | 69 | empty |
| 3 | 426 | 0.72 | 0.82 | 47 | MG, X4C |
| 4 | 107 | 0.39 | 0.76 | 23 | empty |
| 5 | 92 | 0.39 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 839 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3WS8 · Crystal structure of PDE10A in complex with a benzimidazole inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y233 · AlphaFold monomer V2.0 prediction for camp and camp-inhibited cgmp 3',5'-cyclic… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9Y233
- Elsewhere: RCSB PDB 3WS8 · PDBe 3WS8 · UniProt Q9Y233
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