SMTL ID : 7qkn.1 (1 other biounit)

Crystal structure of YTHDF1 YTH domain in complex with the ebsulfur derivative compound 7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x JVF: ~{N}-[2-(diethylamino)ethyl]-2-sulfanyl-benzamide(Non-covalent)

JVF.1: 6 residues within 4Å: Chain A: D.42, R.45, S.46, I.51, W.52, C.53 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.45, A:W.52 Hydrogen bonds: A:D.42 Salt bridges: A:D.42

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: H.16, Y.18, I.47, S.50, V.117, Q.118, W.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.47, A:V.117, A:W.119 EDO.3: 4 residues within 4Å: Chain A: H.6, E.181, K.182, A.185 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.181

1 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.4: 6 residues within 4Å: Chain A: E.40, I.43, V.81, S.84, H.86, I.173 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Micaelli, M. et al., Small-Molecule Ebselen Binds to YTHDF Proteins Interfering with the Recognition of N 6 -Methyladenosine-Modified RNAs. Acs Pharmacol Transl Sci (2022)

Release Date

2022-11-23

Peptides

YTH domain-containing family protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

YTH domain-containing family protein 1

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