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

Crystal structure of YTHDC1 with compound DHU_DC1_068

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x P0K: 6-[[furan-2-ylmethyl(methyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione(Non-covalent)

P0K.1: 16 residues within 4Å: Chain A: I.34, K.35, S.36, N.37, N.41, W.51, S.52, T.53, L.54, R.78, W.102, L.104, P.105, M.108, L.113, D.150 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.54, A:L.113 Hydrogen bonds: A:R.78, A:R.78, A:D.150 Water bridges: A:L.54, A:L.54, A:D.150, A:D.150

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 4 residues within 4Å: Chain A: K.21, D.173, L.174, Y.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.21, A:L.174 Water bridges: A:K.21

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

SO4.3: 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:R.78, A:R.149 Salt bridges: A:K.35, A:R.78, A:R.149 SO4.4: 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 SO4.5: 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 Water bridges: A:S.93 Salt bridges: A:H.95 SO4.6: 3 residues within 4Å: Chain A: K.59, N.62, R.66 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.62 Water bridges: A:K.59, A:K.59, A:R.66 Salt bridges: A:K.59, A:R.66 SO4.7: 3 residues within 4Å: Chain A: N.38, H.39, E.40 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.39, A:E.40 Water bridges: A:E.40

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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