MolNFT v1 · #117611 · protein
Human PDE10A in complex with 1-(4-chloro-phenyl)-3-methyl-1H-THIENO[2, 3-C]PYRAZOLE-5-carboxylic acid (tetrahydro-furan-2-ylmethyl)-amide at 2.2A
5EDE · Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase…: “Human PDE10A in complex with 1-(4-chloro-phenyl)-3-methyl-1H-THIENO[2, 3-C]PYRAZOLE-5-carboxylic acid…”. X-ray diffraction, 3 ligands (5M6, ZN, MG), 16 pockets (best…
- PDB
- 5EDE
- Type
- protein
- Length
- 1,255 residues
- Chains
- 4
- 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
- 5M6, ZN, MG
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 4 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 | 314 | 71% 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 | 315 | 71% helix, 0% strand | Q9Y233 |
| C | Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase 10A (EC 3.1.4.17, 3.1.4.35) | protein | 313 | 71% helix, 0% strand | Q9Y233 |
| D | Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase 10A (EC 3.1.4.17, 3.1.4.35) | protein | 313 | 71% helix, 0% strand | Q9Y233 |
Ligands and binding sites
- 5M6 · 1-(4-chlorophenyl)-3-methyl-~{N}-[[(2~{R})-oxolan-2-yl]methyl]thieno[2,3-c]pyrazole-5-carboxamide · 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
- GOL · Glycerol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.77 | 0.79 | 107 | empty |
| 2 | 457 | 0.73 | 0.82 | 46 | MG, 5M6 |
| 3 | 454 | 0.73 | 0.82 | 48 | MG, 5M6 |
| 4 | 430 | 0.73 | 0.83 | 54 | MG, 5M6 |
| 5 | 409 | 0.73 | 0.83 | 44 | MG, 5M6 |
Interfaces
5 interfaces between chains.
- A–B · 700 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 696 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 682 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 475 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 47 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 3 disulfide (artifact, disulfide).
Compared structures
- 5EDE · CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 10 IN COMPLEX 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 5EDE · PDBe 5EDE · UniProt Q9Y233
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.