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

Crystal structure of YTHDC1 with compound T96

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

1 x OWH: ~{N}-methylpyridine-3-carbothioamide(Non-covalent)

OWH.1: 12 residues within 4Å: Chain A: N.37, N.41, W.51, S.52, T.53, L.54, W.102, L.104, P.105, M.108, L.113, D.150 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.113 Hydrogen bonds: A:S.52, A:T.53, A:L.54

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

SO4.2: 3 residues within 4Å: Chain A: N.37, P.105, A.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.37, A:A.106 SO4.3: 3 residues within 4Å: Chain A: S.93, H.94, H.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.95 Salt bridges: A:H.94 SO4.4: 4 residues within 4Å: Chain A: G.18, T.19, S.20, K.21 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.20, A:S.20, A:K.21 Water bridges: A:T.19, A:K.21, A:K.21, A:L.22 Salt bridges: A:K.21 SO4.5: 3 residues within 4Å: Chain A: R.78, R.149, D.150 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:R.78, A:R.78, A:R.78, A:D.150 Salt bridges: A:R.78

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
A

YTH domain-containing protein 1

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