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CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 10 IN COMPLEX WITH c4c(c1cn(c(n1)CCc2cccc3nccnc23)C)cccc4, micromolar IC50=0.48281
Analyse CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 10 IN COMPLEX WITH… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SJV
- Type
- protein
- Length
- 1,251 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.94
- Source
- Homo sapiens
- Molecule
- cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
- EC
- 3.1.4.17
- UniProt
- Q9Y233
- Ligands
- K9F, ZN, MG
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · resolution 1.94 · 3 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A (EC 3.1.4.17) | protein | 313 | 71% helix, 0% strand | Q9Y233 |
| B | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A (EC 3.1.4.17) | protein | 315 | 71% helix, 0% strand | Q9Y233 |
| D | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A (EC 3.1.4.17) | protein | 310 | 72% helix, 0% strand | Q9Y233 |
Ligands and binding sites
- K9F · 5-[2-(1-methyl-4-phenyl-1H-imidazol-2-yl)ethyl]quinoxaline · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.73 | 0.79 | 79 | empty |
| 2 | 426 | 0.73 | 0.83 | 45 | MG, K9F |
| 3 | 466 | 0.72 | 0.82 | 51 | MG, K9F |
| 4 | 423 | 0.72 | 0.82 | 44 | MG, K9F |
| 5 | 399 | 0.71 | 0.82 | 44 | MG, K9F |
Interfaces
5 interfaces between chains.
- A–B · 712 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 709 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 695 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 497 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 50 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 modified (disulfide, artifact).
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 5SJV · PDBe 5SJV · UniProt Q9Y233
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