Research workbench
Crystal structure of PDE10A with 1H-benzimidazol-2-YL(4-((3- (tetrahydro-2H-pyran-4-yl)-2-PYRIDINYL)OXY)PHENYL)METHANONE
Analyse Crystal structure of PDE10A with 1H-benzimidazol-2-YL(4-((3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PHW
- Type
- protein
- Length
- 610 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
- 2W1, ZN, SO4
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 73% 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 | 305 | 73% helix, 0% strand | Q9Y233 |
Ligands and binding sites
- 2W1 · 1H-benzimidazol-2-yl(4-{[3-(tetrahydro-2H-pyran-4-yl)pyridin-2-yl]oxy}phenyl)methanone · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.73 | 0.83 | 41 | ZN, 2W1 |
| 2 | 484 | 0.73 | 0.82 | 55 | ZN, 2W1 |
| 3 | 258 | 0.60 | 0.80 | 39 | empty |
| 4 | 119 | 0.54 | 0.83 | 28 | empty |
| 5 | 87 | 0.51 | 0.84 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 585 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4PHW · Crystal Structure of PDE10A with 1H-benzimidazol-2-yl(4-((3-(tetrahydro-2H-pyran-4-yl)-2-p… · 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 4PHW · PDBe 4PHW · UniProt Q9Y233
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