SMTL ID : 7p8b.2 (1 other biounit)

Crystal structure of YTHDC1 with compound YLI_DC1_006

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

2 x OYT: 9-cyclopropyl-~{N}-methyl-purin-6-amine(Non-covalent)

OYT.1: 13 residues within 4Å: Chain A: K.35, S.36, N.37, N.41, W.51, S.52, T.53, W.102, P.105, M.108, L.113, D.150 Ligands: SO4.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.37, A:N.41, A:S.52 OYT.2: 2 residues within 4Å: Chain A: P.99, H.101 3 PLIP interactions: 3 interactions with chain A Water bridges: A:I.100 pi-Stacking: A:H.101, A:H.101

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

SO4.3: 2 residues within 4Å: Chain A: R.125, E.126 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.126 Water bridges: A:R.125, A:R.125, A:R.125 Salt bridges: A:R.125 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: 3 residues within 4Å: Chain A: R.149, D.150 Ligands: OYT.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.150 Salt bridges: A:R.149 SO4.6: 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 SO4.7: 3 residues within 4Å: Chain A: K.59, N.62, R.66 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.62 Water bridges: A:K.59 Salt bridges: A:K.59, A:R.66

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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