MolNFT v1 · #110479 · protein
Crystal structure of PDE10A in complex with ASP9436
4XY2 · Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase…: “Crystal structure of PDE10A in complex with ASP9436”. X-ray diffraction, 3 ligands (490, ZN, MG), 7 pockets (best druggability 0.74). MolNFT v1 #110479 on GenesisL1: 3D…
- PDB
- 4XY2
- Type
- protein
- Length
- 634 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
- 490, ZN, MG
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 71% 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 | 312 | 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 | 322 | 73% helix, 0% strand | Q9Y233 |
Ligands and binding sites
- 490 · 1-methyl-5-(1-methyl-3-{[4-(1-methyl-1H-benzimidazol-4-yl)phenoxy]methyl}-1H-pyrazol-4-yl)pyridin-2(1H)-one · 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
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 | 512 | 0.74 | 0.82 | 55 | MG |
| 2 | 628 | 0.74 | 0.80 | 60 | MG, 490 |
| 3 | 695 | 0.71 | 0.78 | 59 | empty |
| 4 | 58 | 0.53 | 0.88 | 18 | empty |
| 5 | 120 | 0.41 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 823 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4XY2 · Crystal structure of PDE10A in complex with ASP9436 · 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 4XY2 · PDBe 4XY2 · UniProt Q9Y233
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