SMTL ID : 6ynk.1 (1 other biounit)

Crystal structure of YTHDC1 with compound DHU_DC1_068

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x P0K: 6-[[furan-2-ylmethyl(methyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione(Non-covalent)

P0K.1: 13 residues within 4Å: Chain A: K.35, S.36, N.37, N.41, W.51, S.52, T.53, L.54, R.78, W.102, M.108, L.113, D.150 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.54, A:L.113 Hydrogen bonds: A:R.78, A:R.78, A:D.150 Water bridges: A:L.54, A:L.54, A:L.54, A:N.57, A:D.150, A:D.150

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

SO4.2: 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 Water bridges: A:R.78 Salt bridges: A:R.78 SO4.3: 4 residues within 4Å: Chain A: K.60, W.139, Q.152, E.153 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.152, A:E.153 Water bridges: A:Q.152, A:Q.152 Salt bridges: A:K.60 SO4.4: 4 residues within 4Å: Chain A: G.18, T.19, S.20, K.21 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.18, A:S.20, A:K.21 Water bridges: A:T.19, A:L.22 Salt bridges: A:K.21

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
A

YTHDC1

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