SMTL ID : 7p8f.2 (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

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

SO4.1: 2 residues within 4Å: Chain A: R.125, E.126 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.126 Water bridges: A:R.125, A:R.125 Salt bridges: A:R.125 SO4.3: 3 residues within 4Å: Chain A: G.151, Q.152, E.153 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.152, A:E.153 Water bridges: A:G.151 SO4.4: 1 residues within 4Å: Chain A: R.125 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.125 Salt bridges: A:R.125 SO4.5: 3 residues within 4Å: Chain A: R.149, D.150 Ligands: 5ZK.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:D.150, A:D.150 Salt bridges: A:R.149 SO4.6: 1 residues within 4Å: Chain A: K.131 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.131, A:K.131 Salt bridges: A:K.131

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

5ZK.2: 11 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 Ligands: SO4.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.37, A:N.41, A:S.52, A:S.52

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

Related Entries With Identical Sequence