Research workbench
Crystal structure of PDE10A in complex with a triazolopyrimidine inhibitor
Analyse Crystal structure of PDE10A in complex with a triazolopyrimidine inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KDZ
- Type
- protein
- Length
- 648 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
- D79, ZN, MG
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 70% 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 | 70% helix, 0% strand | Q9Y233 |
Ligands and binding sites
- D79 · 4-[2-(5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)ethyl]-3,7,8,10-tetrazatricyclo[7.4.0.0^{2, 7}]trideca-1,3,5,8,10,12-hexaen-6-ol · ligand · chains A
- 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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 718 | 0.76 | 0.80 | 64 | MG, D79 |
| 2 | 459 | 0.72 | 0.82 | 50 | MG |
| 3 | 558 | 0.71 | 0.80 | 48 | empty |
| 4 | 83 | 0.59 | 0.88 | 22 | empty |
| 5 | 173 | 0.44 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 918 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6KDZ · Crystal structure of PDE10A in complex with a triazolopyrimidine 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 6KDZ · PDBe 6KDZ · UniProt Q9Y233
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