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

Crystal structure of YTHDF2 in complex with compound 5 (AI-DF2-36)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

1 x 01: 2-(methylamino)pyridine-3-carboxamide

01.1: 12 residues within 4Å: Chain A: K.31, S.32, Y.33, S.34, D.37, W.47, C.48, S.49, T.50, W.101, W.106, D.143 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.37, A:C.48, A:D.143 pi-Stacking: A:Y.33, A:W.106

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

SO4.2: 10 residues within 4Å: Chain A: K.31, S.75, V.76, N.77, G.78, S.79, G.80, H.81, N.122, T.139 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.75, A:G.78, A:S.79, A:G.80, A:H.81, A:N.122 Water bridges: A:K.31, A:K.31 Salt bridges: A:K.31 SO4.3: 2 residues within 4Å: Chain A: Q.103, D.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.103, A:D.104, A:D.104 Water bridges: A:K.105 SO4.4: 1 residues within 4Å: Chain A: K.151 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.151 SO4.5: 3 residues within 4Å: Chain A: T.50, E.51, H.52 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.50, A:E.51, A:H.52 Salt bridges: A:H.52

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 2 residues within 4Å: Chain A: N.122, R.126 Ligand excluded by PLIP

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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