SMTL ID : 7z8x.1 (1 other biounit)

Crystal structure of YTHDF2 with compound YLI_DC1_017

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

monomer

Ligands

1 x IGX: 6-methoxy-1H-pyrimidine-2,4-dione(Non-covalent)

IGX.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 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.47 Hydrogen bonds: A:K.31, A:Y.33, A:S.34, A:D.37, A:D.37 Water bridges: A:S.102, A:S.102 pi-Stacking: A:W.106, A:W.106

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

SO4.2: 2 residues within 4Å: Chain A: K.43, Y.44 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.43 SO4.3: 9 residues within 4Å: Chain A: K.31, S.75, V.76, N.77, G.78, S.79, G.80, 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:T.139 Salt bridges: A:K.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nai, F. et al., Fragment Ligands of the m 6 A-RNA Reader YTHDF2. Acs Med.Chem.Lett. (2022)

Release Date

2022-04-06

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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