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

Crystal structure of YTHDC1 with compound DHU_DC1_234

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

1 x OW8: ~{N}-methyl-1,4,5,6-tetrahydrocyclopenta[c]pyrazole-3-carboxamide(Non-covalent)

OW8.1: 9 residues within 4Å: Chain A: K.35, N.37, N.41, W.51, S.52, W.102, P.105, L.113, D.150 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.105 Hydrogen bonds: A:N.41, A:S.52, A:D.150

4 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: R.125, P.167, P.168 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.125, A:R.125, A:R.125, A:R.125 Salt bridges: A:R.125 SO4.4: 4 residues within 4Å: Chain A: K.35, R.78, E.79, R.149 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.79 Water bridges: A:K.35, A:K.35, A:K.35, A:K.35 Salt bridges: A:K.35, A:R.149 SO4.5: 2 residues within 4Å: Chain A: R.149, D.150 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:R.149, A:R.149 Salt bridges: 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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