Research workbench
Crystal structure of YTHDC1 with compound DHU_DC1_068
Analyse Crystal structure of YTHDC1 with compound DHU_DC1_068 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YNK
- Type
- protein
- Length
- 325 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- YTHDC1
- UniProt
- Q96MU7
- Ligands
- P0K, SO4
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | YTHDC1 | protein | 161 | 35% helix, 25% strand | Q96MU7 |
| B | YTHDC1 | protein | 164 | 34% helix, 26% strand | Q96MU7 |
Ligands and binding sites
- P0K · 6-[[furan-2-ylmethyl(methyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.62 | 0.87 | 18 | P0K |
| 2 | 110 | 0.56 | 0.84 | 18 | P0K |
| 3 | 85 | 0.47 | 0.81 | 18 | empty |
| 4 | 104 | 0.44 | 0.78 | 15 | empty |
| 5 | 98 | 0.40 | 0.76 | 18 | PEG |
Interfaces
1 interface between chains.
- A–B · 249 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6YNK · Crystal structure of YTHDC1 with compound DHU_DC1_068 · 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 Q96MU7
- Elsewhere: RCSB PDB 6YNK · PDBe 6YNK · UniProt Q96MU7
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