MolNFT v1 · #114844 · protein
PDE10 complexed with 4,6-dichloro-2-cyclopropyl-5-methyl-pyrimidine
5C1W · Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase…: “PDE10 complexed with 4,6-dichloro-2-cyclopropyl-5-methyl-pyrimidine”. X-ray diffraction, 3 ligands (4XS, ZN, MG), 8 pockets (best druggability 0.71). MolNFT v1 #114844…
- PDB
- 5C1W
- Type
- protein
- Length
- 639 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
- 4XS, ZN, MG
- Pockets
- 8 · best druggability 0.71
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 | 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 | 314 | 68% helix, 0% strand | Q9Y233 |
Ligands and binding sites
- 4XS · 4,6-dichloro-2-cyclopropyl-5-methylpyrimidine · ligand · chains A
- 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.71 | 0.77 | 67 | empty |
| 2 | 390 | 0.70 | 0.82 | 46 | MG, 4XS |
| 3 | 427 | 0.68 | 0.80 | 45 | MG |
| 4 | 57 | 0.48 | 0.85 | 18 | empty |
| 5 | 84 | 0.40 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 931 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5C1W · PDE10 complexed with 4,6-dichloro-2-cyclopropyl-5-methyl-pyrimidine · 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 5C1W · PDBe 5C1W · UniProt Q9Y233
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