SMTL ID : 7pjp.2 (1 other biounit)

Crystal structure of YTHDC1 with compound DHU_DC1_226

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

monomer

Ligands

1 x 7SL: 5-(furan-2-yl)-N-methyl-1H-pyrazole-3-carboxamide(Non-covalent)

7SL.1: 11 residues within 4Å: Chain A: K.35, N.37, N.41, W.51, S.52, L.54, R.78, W.102, L.113, D.150 Ligands: SO4.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.54, A:D.150 Hydrogen bonds: A:N.41, A:S.52, A:D.150 pi-Cation interactions: A:R.78

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

SO4.2: 2 residues within 4Å: Chain A: R.125, E.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.126 Water bridges: A:R.125 Salt bridges: A:R.125 SO4.3: 4 residues within 4Å: Chain A: R.78, R.149, D.150 Ligands: 7SL.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.150 Salt bridges: A:R.78 SO4.4: 2 residues within 4Å: Chain A: G.18, K.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.18 Salt bridges: A:K.21 SO4.5: 2 residues within 4Å: Chain A: R.125, P.167 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.125 Salt bridges: A:R.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Structure-based design of ligands of the m6A-RNA reader YTHDC1. Eur J Med Chem Rep (2022)

Release Date

2021-10-20

Peptides

YTH domain-containing protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

YTH domain-containing protein 1

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