SMTL ID : 8q33.2 (1 other biounit)

Crystal structure of YTHDC1 in complex with Compound 15 (ZA_343)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

monomer

Ligands

1 x IWV: ~{N}-[2-[[2-chloranyl-6-(methylamino)purin-9-yl]methyl]phenyl]-2,2,2-tris(fluoranyl)ethanamide(Non-covalent)

IWV.1: 13 residues within 4Å: Chain A: K.18, S.19, N.20, N.21, N.24, W.34, S.35, L.37, W.85, P.88, L.96, R.132, D.133 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.37, A:P.88 Hydrogen bonds: A:N.20, A:N.24, A:S.35 Water bridges: A:N.20, A:D.133

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

SO4.2: 2 residues within 4Å: Chain A: R.108, E.109 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.109 Water bridges: A:R.108, A:R.108 Salt bridges: A:R.108 SO4.3: 1 residues within 4Å: Chain A: R.108 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zalesak, F. et al., Structure-Based Design of a Potent and Selective YTHDC1 Ligand. J.Med.Chem. (2024)

Release Date

2023-12-06

Peptides

YTH domain-containing protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

YTH domain-containing protein 1

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