MolNFT v1 · #114862 · protein
PDE10 complexed WITH6-chloro-N-[(2,4-dimethylthiazol-5-YL)METHYL]-5- methyl-2-[2-(2-PYRIDYL)ETHOXY]PYRIMIDIN-4-amine
5C2E · Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase…: “PDE10 complexed WITH6-chloro-N-[(2,4-dimethylthiazol-5-YL)METHYL]-5…”. X-ray diffraction, 4 ligands (4PX, 4Y1, ZN), 6 pockets (best druggability 0.82). MolNFT v1 #114862…
- PDB
- 5C2E
- Type
- protein
- Length
- 646 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
- 4PX, 4Y1, ZN, MG
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase 10A (EC 3.1.4.17, 3.1.4.35) | protein | 323 | 72% helix, 0% strand | Q9Y233 |
Ligands and binding sites
- 4PX · 3-(1-hydroxy-2-methylpropan-2-yl)-5-phenyl-3,5-dihydro-1H-imidazo[4,5-c][1,8]naphthyridine-2,4-dione · ligand · chains A, B
- 4Y1 · 6-chloro-N-[(2,4-dimethyl-1,3-thiazol-5-yl)methyl]-5-methyl-2-[2-(pyridin-2-yl)ethoxy]pyrimidin-4-amine · ligand · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 860 | 0.82 | 0.84 | 75 | MG, 4PX |
| 2 | 538 | 0.72 | 0.80 | 52 | MG, 4Y1 |
| 3 | 54 | 0.62 | 0.93 | 22 | empty |
| 4 | 50 | 0.58 | 0.92 | 20 | empty |
| 5 | 52 | 0.31 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 435 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5C2E · PDE10 complexed with6-chloro-N-[(2,4-dimethylthiazol-5-yl)methyl]-5-methyl-2-[2-(2-pyridyl… · 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 5C2E · PDBe 5C2E · UniProt Q9Y233
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