Research workbench
CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 10 IN COMPLEX WITH c13c(ccc2c1nccc2)[nH]c(n3)SCc4ncc(c(c4C)OC)C, micromolar IC50=0.046043
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
- 5SHP
- Type
- protein
- Length
- 1,251 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.18
- Source
- Homo sapiens
- Molecule
- cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
- EC
- 3.1.4.17
- UniProt
- Q9Y233
- Ligands
- JIG, ZN, MG
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.18 · 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 | 71% helix, 0% strand | Q9Y233 |
Ligands and binding sites
- JIG · 2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfanyl}-1H-imidazo[4,5-h]quinoline · 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
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.75 | 0.79 | 88 | empty |
| 2 | 459 | 0.74 | 0.83 | 48 | MG, JIG |
| 3 | 457 | 0.74 | 0.83 | 54 | MG, JIG |
| 4 | 455 | 0.73 | 0.83 | 49 | MG, JIG |
| 5 | 468 | 0.73 | 0.82 | 54 | MG, JIG |
Interfaces
5 interfaces between chains.
- B–C · 714 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 706 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 698 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 491 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 55 Ų buried · 1 hydrogen bond · 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 5SHP · PDBe 5SHP · UniProt Q9Y233
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