SMTL ID : 7p8f.1 (1 other biounit)

Crystal structure of YTHDC1 with compound YLI_DC1_008

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x 5ZK: ~{N},3-dimethyl-1~{H}-pyrazolo[4,3-d]pyrimidin-7-amine(Non-covalent)

5ZK.1: 10 residues within 4Å: Chain A: K.35, S.36, N.37, N.41, W.51, S.52, W.102, P.105, L.113, D.150 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.37, A:N.41, A:S.52 Water bridges: A:W.51, A:T.53, A:D.150

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

SO4.2: 5 residues within 4Å: Chain A: K.60, W.139, G.151, Q.152, E.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.152, A:E.153 Water bridges: A:E.153 Salt bridges: A:K.60

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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