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

Crystal structure of YTHDC1 with compound PSI_DC1_004

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x 7RX: (R)-homoproline(Non-covalent)

7RX.1: 9 residues within 4Å: Chain A: N.41, W.51, S.52, T.53, L.54, W.102, M.108, D.150 Ligands: SO4.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.102 Hydrogen bonds: A:L.54, A:D.150 Water bridges: A:T.53

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 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, A:R.66, A:R.66 Water bridges: A:S.93

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

SO4.3: 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 SO4.4: 6 residues within 4Å: Chain A: S.36, N.37, N.38, N.41, W.51 Ligands: 7RX.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.36, A:N.37, A:N.37, A:N.38, A:N.41 SO4.5: 2 residues within 4Å: Chain A: G.18, K.21 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.18 Water bridges: A:K.21, A:K.21 Salt bridges: A:K.21 SO4.6: 3 residues within 4Å: Chain A: R.78, R.149, D.150 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:N.37 Salt bridges: A:R.78, A:R.149 SO4.7: 1 residues within 4Å: Chain A: R.125 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.125

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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