MolNFT v1 · #114856 · protein
PDE10 complexed with 6-chloro-2-cyclopropyl-5-methyl-pyrimidin-4-amine
5C28 · Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase…: “PDE10 complexed with 6-chloro-2-cyclopropyl-5-methyl-pyrimidin-4-amine”. X-ray diffraction, 3 ligands (4XV, ZN, MG), 6 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 5C28
- Type
- protein
- Length
- 642 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
- 4XV, ZN, MG
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 70% 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 | 325 | 72% 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 | 317 | 69% helix, 0% strand | Q9Y233 |
Ligands and binding sites
- 4XV · 6-chloro-2-cyclopropyl-5-methylpyrimidin-4-amine · ligand · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.80 | 0.83 | 100 | MG, 4XV |
| 2 | 217 | 0.64 | 0.83 | 28 | empty |
| 3 | 103 | 0.44 | 0.78 | 20 | empty |
| 4 | 71 | 0.33 | 0.76 | 13 | empty |
| 5 | 60 | 0.30 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 559 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5C28 · PDE10 complexed with 6-chloro-2-cyclopropyl-5-methyl-pyrimidin-4-amine · 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 5C28 · PDBe 5C28 · UniProt Q9Y233
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