SMTL ID : 6ykj.2 (1 other biounit)

Crystal structure of YTHDC1 with compound DHU_DC1_125

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.125, E.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.126 Water bridges: A:R.125 Salt bridges: A:R.125 SO4.2: 2 residues within 4Å: Chain A: R.125, P.168 3 PLIP interactions: 3 interactions with chain A Water bridges: 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.150 Salt bridges: A:R.78, A:R.149

1 x OUW: ~{N}-methyl-4-(methylamino)pyridine-2-carboxamide(Non-covalent)

OUW.4: 10 residues within 4Å: Chain A: N.37, N.41, W.51, S.52, T.53, L.54, W.102, P.105, L.113, D.150 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.54 Hydrogen bonds: A:N.41, 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

2020-07-15

Peptides

YTHDC1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

YTHDC1

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