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

Crystal structure of YTHDC1 with compound DHU_DC1_046

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x P0N: (2~{R})-2-(2-chlorophenyl)-5,5-dimethyl-morpholine(Non-covalent)

P0N.1: 13 residues within 4Å: Chain A: N.41, W.51, S.52, L.54, W.102, V.103, L.104, P.105, M.108, S.109, M.112, L.113 Ligands: SO4.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.41, A:W.51, A:L.54, A:W.102, A:W.102, A:P.105, A:M.108, A:M.112, A:L.113 Hydrogen bonds: A:S.52

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

SO4.2: 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 SO4.3: 5 residues within 4Å: Chain A: S.36, N.37, N.41, R.78 Ligands: P0N.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.36, A:N.37, A:N.37, A:N.38, A:N.41, A:R.78, A:V.103 SO4.4: 4 residues within 4Å: Chain A: K.60, G.151, Q.152, E.153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.153 Salt bridges: A:K.60 SO4.5: 1 residues within 4Å: Chain A: R.125 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.125, A:E.170 Salt bridges: A:R.125 SO4.6: 3 residues within 4Å: Chain A: R.78, R.149, D.150 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:G.148, A:R.149, A:R.149 Salt bridges: A:R.78, A:R.149

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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