Research workbench
Crystal structure of YTHDF2 with compound YLI_DC1_018
Analyse Crystal structure of YTHDF2 with compound YLI_DC1_018 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Z8W
- Type
- protein
- Length
- 297 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yth domain-containing family protein 2
- UniProt
- Q9Y5A9
- Ligands
- IHR, SO4, CL
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yth domain-containing family protein 2 | protein | 143 | 30% helix, 31% strand | Q9Y5A9 |
| B | Yth domain-containing family protein 2 | protein | 154 | 31% helix, 29% strand | Q9Y5A9 |
Ligands and binding sites
- IHR · ~{N}-cyclopropyl-3-methyl-2~{H}-pyrazolo[4,3-d]pyrimidin-7-amine · ligand · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.52 | 0.86 | 22 | IHR |
| 2 | 101 | 0.47 | 0.80 | 22 | IHR |
Interfaces
1 interface between chains.
- A–B · 425 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7Z8W · Crystal structure of YTHDF2 with compound YLI_DC1_018 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y5A9 · AlphaFold monomer V2.0 prediction for yth domain-containing family protein 2 (Q9Y5A9) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9Y5A9
- Elsewhere: RCSB PDB 7Z8W · PDBe 7Z8W · UniProt Q9Y5A9
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