MolNFT v1 · #114179 · protein
Crystal structure of the catalytic domain of human PDE10A complexed with N-(4-((5-methyl-5H-PYRROLO[3,2-D]PYRIMIDIN-4-YL)OXY)PHENYL)-1H- benzimidazol-2-amine
5B4K · 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 (6DT, MG, ZN), 7 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 5B4K
- 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
- 6DT, MG, ZN
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 71% 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 | 72% helix, 0% strand | Q9Y233 |
Ligands and binding sites
- 6DT · N-(4-((5-methyl-5H-pyrrolo[3,2-d]pyrimidin-4-yl)oxy)phenyl)-1H-benzimidazol-2-amine · 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.73 | 0.84 | 40 | MG, 6DT |
| 2 | 769 | 0.73 | 0.78 | 62 | empty |
| 3 | 558 | 0.72 | 0.80 | 62 | MG, 6DT |
| 4 | 94 | 0.38 | 0.76 | 20 | empty |
| 5 | 76 | 0.36 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 860 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5B4K · 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 5B4K · PDBe 5B4K · UniProt Q9Y233
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