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

Crystal structure of YTHDC1 with compound T96C1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

monomer

Ligands

1 x PJH: ~{N}-methylpyridine-3-carboxamide(Non-covalent)

PJH.1: 9 residues within 4Å: Chain A: N.41, W.51, S.52, T.53, L.54, W.102, M.108, L.113, D.150 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.113 Hydrogen bonds: A:N.41, A:S.52, A:T.53, A:L.54

3 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: 1 residues within 4Å: Chain A: R.125 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.125, A:R.125 Salt bridges: A:R.125 SO4.4: 4 residues within 4Å: Chain A: R.78, G.148, R.149, D.150 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:R.78, A:R.149 Salt bridges: A:R.78, A:R.149

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: R.30, F.31, W.139, E.153, I.154 Ligand excluded by PLIP

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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