MolNFT v1 · #83962 · protein
Crystal structure of the catalytic domain of PDE10A complexed with 5- methoxy-3-(1-phenyl-1H-pyrazol-5-yl)-1-(3-(TRIFLUOROMETHYL)PHENYL) pyridazin-4(1H)-one
3WYL · Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase…: “Crystal structure of the catalytic domain of PDE10A complexed with 5…”. X-ray diffraction, 3 ligands (3KB, ZN, MG), 6 pockets (best druggability 0.74). MolNFT v1 #83962…
- PDB
- 3WYL
- Type
- protein
- Length
- 628 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
- 3KB, ZN, MG
- Pockets
- 6 · 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 | 315 | 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 | 313 | 72% helix, 0% strand | Q9Y233 |
Ligands and binding sites
- 3KB · 5-methoxy-3-(1-phenyl-1H-pyrazol-5-yl)-1-[3-(trifluoromethyl)phenyl]pyridazin-4(1H)-one · 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.74 | 0.80 | 69 | MG, 3KB |
| 2 | 449 | 0.74 | 0.83 | 54 | MG, 3KB |
| 3 | 613 | 0.71 | 0.79 | 51 | empty |
| 4 | 90 | 0.36 | 0.75 | 17 | empty |
| 5 | 57 | 0.31 | 0.76 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 826 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3WYL · Crystal structure of the catalytic domain of PDE10A complexed with… · 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 3WYL · PDBe 3WYL · UniProt Q9Y233
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