Research workbench
Crystal structure of PDE10A with novel keto-benzimidazole inhibitor
Analyse Crystal structure of PDE10A with novel keto-benzimidazole inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MVH
- Type
- protein
- Length
- 615 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase 10A
- EC
- 3.1.4.17, 3.1.4.35
- UniProt
- Q9Y233
- Ligands
- 2F5, ZN, SO4
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 72% 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 | 307 | 73% 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 | 308 | 71% helix, 0% strand | Q9Y233 |
Ligands and binding sites
- 2F5 · 1H-benzimidazol-2-yl(4-{[3-(morpholin-4-yl)pyrazin-2-yl]oxy}phenyl)methanone · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.73 | 0.83 | 47 | ZN, 2F5 |
| 2 | 400 | 0.73 | 0.83 | 47 | ZN, 2F5 |
| 3 | 265 | 0.65 | 0.82 | 39 | empty |
| 4 | 88 | 0.55 | 0.85 | 20 | empty |
| 5 | 132 | 0.52 | 0.81 | 29 | SO4 |
Interfaces
1 interface between chains.
- A–B · 595 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4MVH · Crystal Structure of PDE10A with Novel Keto-Benzimidazole 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 Q9Y233
- Elsewhere: RCSB PDB 4MVH · PDBe 4MVH · UniProt Q9Y233
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