MolNFT v1 · #186204 · protein
Crystal structure of YTHDF2 with compound YLI_DF_029
7R5W · Yth domain-containing family protein 2: “Crystal structure of YTHDF2 with compound YLI_DF_029”. X-ray diffraction, 3 ligands (I5Z, SO4, CL), 3 pockets (best druggability 0.54). MolNFT v1 #186204 on GenesisL1: 3D structure, binding…
- PDB
- 7R5W
- Type
- protein
- Length
- 299 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
- I5Z, SO4, CL
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yth domain-containing family protein 2 | protein | 149 | 31% helix, 30% strand | Q9Y5A9 |
| B | Yth domain-containing family protein 2 | protein | 150 | 29% helix, 29% strand | Q9Y5A9 |
Ligands and binding sites
- I5Z · 6-cyclopropyl-1H-pyrimidine-2,4-dione · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.54 | 0.84 | 25 | I5Z |
| 2 | 115 | 0.49 | 0.80 | 31 | SO4, I5Z, GOL |
| 3 | 51 | 0.41 | 0.82 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 498 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7R5W · Crystal structure of YTHDF2 with compound YLI_DF_029 · 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 B against A, TM-score 0.96
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 7R5W · PDBe 7R5W · UniProt Q9Y5A9
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