MolNFT v1 · #116548 · protein
PDE10 complexed with N-[(1-methylpyrazol-4-YL)METHYL]-5-[[(1S,2S)-2- (2-PYRIDYL)CYCLOPROPYL]METHOXY]PYRAZOLO[1,5-A]PYRIMIDIN-7-amine
5DH5 · Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase…: “PDE10 complexed with N-[(1-methylpyrazol-4-YL)METHYL]-5-[[(1S,2S)-2…”. X-ray diffraction, 3 ligands (5AY, ZN, MG), 7 pockets (best druggability 0.82). MolNFT v1 #116548…
- PDB
- 5DH5
- Type
- protein
- Length
- 644 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
- 5AY, ZN, MG
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 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 | 321 | 69% 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 | 323 | 71% helix, 0% strand | Q9Y233 |
Ligands and binding sites
- 5AY · N-[(1-methyl-1H-pyrazol-4-yl)methyl]-5-{[(1S,2S)-2-(pyridin-2-yl)cyclopropyl]methoxy}pyrazolo[1,5-a]pyrimidin-7-amine · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.82 | 0.84 | 75 | MG, 5AY |
| 2 | 548 | 0.72 | 0.80 | 62 | MG, 5AY |
| 3 | 54 | 0.61 | 0.93 | 21 | empty |
| 4 | 60 | 0.55 | 0.89 | 21 | empty |
| 5 | 62 | 0.49 | 0.84 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 426 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5DH5 · PDE10 complexed with N-[(1-methylpyrazol-4-yl)methyl]-5-[[(1S,2S)-2-(2-pyridyl)cyclopropyl… · 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 5DH5 · PDBe 5DH5 · UniProt Q9Y233
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