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

Crystal structure of YTHDC1 with compound DHU_DC1_092

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

2 x OUZ: ~{N}-ethyl-2-[(2~{S},5~{R})-5-methyl-2-phenyl-morpholin-4-yl]ethanamine(Non-covalent)

OUZ.1: 11 residues within 4Å: Chain A: N.41, W.51, S.52, L.54, W.102, P.105, M.108, S.109, M.112, L.113 Ligands: SO4.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.51, A:L.54, A:W.102, A:P.105, A:M.108, A:M.112, A:L.113 Water bridges: A:W.51, A:S.52 OUZ.2: 2 residues within 4Å: Chain A: Y.24, I.178 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.24, A:Y.24

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: 3 residues within 4Å: Chain A: S.93, H.94, H.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.95 Salt bridges: A:H.94, A:H.95 SO4.5: 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:D.150 Salt bridges: A:R.78, A:R.149 SO4.6: 6 residues within 4Å: Chain A: S.36, N.37, N.38, N.41, W.51 Ligands: OUZ.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 SO4.7: 3 residues within 4Å: Chain A: K.59, N.62, R.66 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.62 Water bridges: A:K.59, A:K.59, A:K.59, A:R.66, A:R.66, A:E.92, A:E.92 Salt bridges: A:K.59, A:R.66

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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