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

Crystal structure of YTHDC1 with compound DHU_DC1_078

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x P0Z: 3-[(2~{R})-5,5-dimethyl-2-phenyl-morpholin-4-yl]-~{N}-(methylcarbamoyl)propanamide(Non-covalent)

P0Z.1: 10 residues within 4Å: Chain A: N.41, W.51, S.52, L.54, W.102, P.105, M.108, S.109, M.112 Ligands: SO4.5 9 PLIP interactions: 9 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 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: 3 residues within 4Å: Chain A: S.93, H.94, H.95 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.95 Water bridges: A:S.93, A:S.93 Salt bridges: A:H.94, A:H.95 SO4.4: 2 residues within 4Å: Chain A: R.149, D.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:D.150 Salt bridges: A:R.149 SO4.5: 6 residues within 4Å: Chain A: S.36, N.37, N.38, N.41, P.105 Ligands: P0Z.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.36, A:N.37, A:N.38, A:N.41 SO4.6: 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 Water bridges: A:K.59 Salt bridges: A:K.59

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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