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Crystal structure of PDE10 in complex with inhibitor 2b
Analyse Crystal structure of PDE10 in complex with inhibitor 2b in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IJI
- Type
- protein
- Length
- 636 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- 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
- AEL, ZN, MG
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.7 · 2 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A (EC 3.1.4.17, 3.1.4.35) | protein | 324 | 70% helix, 0% strand | Q9Y233 |
| B | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A (EC 3.1.4.17, 3.1.4.35) | protein | 312 | 70% helix, 0% strand | Q9Y233 |
Ligands and binding sites
- AEL · 2-{2-[5-methyl-1-(pyridin-4-yl)-1H-benzimidazol-2-yl]ethyl}-1H-benzo[de]isoquinoline-1,3(2H)-dione · ligand · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.75 | 0.81 | 54 | MG, AEL |
| 2 | 421 | 0.73 | 0.83 | 47 | MG |
| 3 | 767 | 0.72 | 0.78 | 57 | empty |
| 4 | 61 | 0.60 | 0.91 | 20 | empty |
| 5 | 108 | 0.41 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 879 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6IJI · Crystal structure of PDE10 in complex with inhibitor 2B · 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 Q9Y233
- Elsewhere: RCSB PDB 6IJI · PDBe 6IJI · UniProt Q9Y233
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