SMTL ID : 9qfl.1 (1 other biounit)

Crystal structure of YTHDF2 in complex with compound 15 (AI-DF2-68)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x 01: 6-sulfanylidene-1,7-dihydropyrazolo[3,4-d]pyrimidin-4-one

01.1: 11 residues within 4Å: Chain A: K.31, S.32, Y.33, S.34, D.37, W.47, C.48, S.49, W.101, W.106, D.143 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.33, A:S.34, A:D.37, A:D.37, A:C.48 Water bridges: A:S.102, A:S.102, A:D.143 pi-Stacking: A:W.106, A:W.106, A:W.106

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: K.31, N.77, G.78, S.79, G.80, N.122, T.139 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.31, A:K.31, A:G.78, A:N.122

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: K.43, Y.44 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.44 Salt bridges: A:K.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Invernizzi, A. et al., Discovery of YTHDF2 Ligands by Fragment-Based Design. Acs Bio Med Chem Au (2025)

Release Date

2025-07-09

Peptides

YTH domain-containing family protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

YTH domain-containing family protein 2

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