MolNFT v1 · #114180 · protein
Crystal structure of the catalytic domain of human PDE10A complexed with 1-(cyclopropylmethyl)-5-(2-(2,3-dihydro-1H-IMIDAZO[1,2- A]BENZIMIDAZOL-1-YL)ETHOXY)-3-(1-phenyl-1H-pyrazol-5-YL)PYRIDAZIN- 4(1H)-one
5B4L · Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase…: “Crystal structure of the catalytic domain of human PDE10A complexed with…”. X-ray diffraction, 3 ligands (6DW, MG, ZN), 6 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 5B4L
- Type
- protein
- Length
- 631 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
- UniProt
- Q9Y233
- Ligands
- 6DW, MG, ZN
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 72% 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) | protein | 315 | 70% helix, 0% strand | Q9Y233 |
| B | Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase 10A (EC 3.1.4.17) | protein | 316 | 73% helix, 0% strand | Q9Y233 |
Ligands and binding sites
- 6DW · 1-(cyclopropylmethyl)-5-(2-(2,3-dihydro-1H-imidazo[1,2-a]benzimidazol-1-yl)ethoxy)-3-(1-phenyl-1H-pyrazol-5-yl)pyridazin-4(1H)-one · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ZN · Zinc 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 | 594 | 0.73 | 0.80 | 66 | MG, 6DW |
| 2 | 407 | 0.72 | 0.83 | 44 | MG, 6DW |
| 3 | 727 | 0.71 | 0.78 | 63 | empty |
| 4 | 72 | 0.35 | 0.76 | 19 | empty |
| 5 | 68 | 0.35 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 848 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5B4L · Crystal structure of the catalytic domain of human 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 5B4L · PDBe 5B4L · UniProt Q9Y233
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