MolNFT v1 · #85666 · protein
Identification and structural characterization of PDE10 fragment inhibitors
4AJG · Camp and camp-inhibited cgmp 3', 5'-cyclic…: “Identification and structural characterization of PDE10 fragment inhibitors”. X-ray diffraction, 3 ligands (F07, ZN, MG), 9 pockets (best druggability 0.72). MolNFT v1 #85666 on…
- PDB
- 4AJG
- Type
- protein
- Length
- 643 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
- F07, ZN, MG
- Pockets
- 9 · best druggability 0.72
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, 3.1.4.35) | protein | 321 | 73% 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 | 322 | 71% helix, 0% strand | Q9Y233 |
Ligands and binding sites
- F07 · Thieno[3,2-c][1,6]naphthyridine · ligand · 2 copies · chains A, D
- ZN · Zinc ion · metal · 2 copies · chains A, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.72 | 0.82 | 50 | MG, F07 |
| 2 | 415 | 0.72 | 0.83 | 46 | MG, F07 |
| 3 | 57 | 0.61 | 0.92 | 20 | empty |
| 4 | 62 | 0.55 | 0.88 | 22 | empty |
| 5 | 159 | 0.54 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–D · 802 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4AJG · Identification and structural characterization of PDE10 fragment inhibitors · 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 4AJG · PDBe 4AJG · UniProt Q9Y233
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