MolNFT v1 · #170890 · protein
Crystal structure of YTHDC1 with compound ADO_AC_89
6YM6: “Crystal structure of YTHDC1 with compound ADO_AC_89”. X-ray diffraction, 2 ligands (OYT, SO4), 4 pockets (best druggability 0.69). MolNFT v1 #170890 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6YM6
- Type
- protein
- Length
- 328 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- YTHDC1
- UniProt
- Q96MU7
- Ligands
- OYT, SO4
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | YTHDC1 | protein | 164 | 32% helix, 24% strand | Q96MU7 |
Ligands and binding sites
- OYT · 9-cyclopropyl-~{N}-methyl-purin-6-amine · ligand · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.69 | 0.85 | 33 | SO4 |
| 2 | 73 | 0.50 | 0.84 | 16 | OYT |
| 3 | 66 | 0.47 | 0.84 | 15 | OYT |
| 4 | 109 | 0.41 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 584 Ų buried · 5 hydrogen bonds · protein-protein
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 Q96MU7
- Elsewhere: RCSB PDB 6YM6 · PDBe 6YM6 · UniProt Q96MU7
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