SMTL ID : 7pj9.2 (1 other biounit)

Crystal structure of YTHDC1 with compound DHU_DC1_232

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

1 x 7RI: 5-bromanyl-N-methyl-1H-indazole-3-carboxamide(Non-covalent)

7RI.1: 9 residues within 4Å: Chain A: K.35, N.41, W.51, S.52, T.53, R.78, W.102, L.113, D.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.41, A:S.52, A:D.150

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

SO4.2: 2 residues within 4Å: Chain A: R.125, E.126 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.126 Water bridges: A:R.125, A:R.125, A:R.125, A:R.125, A:R.125 Salt bridges: A:R.125 SO4.3: 3 residues within 4Å: Chain A: R.78, R.149, D.150 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:R.78, A:R.78 Salt bridges: A:R.78, A:R.149 SO4.4: 3 residues within 4Å: Chain A: S.93, H.94, H.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.95 Salt bridges: A:H.94, A:H.95

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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