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

Crystal structure of YTHDC1 with compound DHU_DC1_096

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

2 x P1Q: 1-[(2~{R},5~{S})-2-(3-chlorophenyl)-5-methyl-morpholin-4-yl]-3-methoxy-propan-2-ol(Non-covalent)

P1Q.1: 12 residues within 4Å: Chain A: N.41, W.51, S.52, L.54, W.102, L.104, P.105, M.108, S.109, M.112, L.113 Ligands: SO4.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.41, A:W.51, A:L.54, A:W.102, A:L.104, A:P.105, A:M.108, A:L.113 Water bridges: A:N.41 Halogen bonds: A:S.109 P1Q.2: 1 residues within 4Å: Chain A: Y.24 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.24 pi-Stacking: A:Y.24

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

SO4.3: 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 SO4.4: 6 residues within 4Å: Chain A: S.36, N.37, N.38, N.41, W.51 Ligands: P1Q.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.36, A:N.37, A:N.37, A:N.38, A:N.41 Water bridges: A:R.78 SO4.5: 2 residues within 4Å: Chain A: G.18, K.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.18 Salt bridges: A:K.21 SO4.6: 2 residues within 4Å: Chain A: R.125, P.167 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.125 SO4.7: 3 residues within 4Å: Chain A: K.59, N.62, R.66 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.62 Water bridges: A:K.59, A:E.92 Salt bridges: A:K.59, A:R.66 SO4.8: 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

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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