SMTL ID : 8q37.2 (1 other biounit)

Crystal structure of YTHDC1 in complex with Compound 18 (ZA_312)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

monomer

Ligands

1 x IWF: 2-chloranyl-9-[(2-methoxyphenyl)methyl]-~{N}-methyl-purin-6-amine(Non-covalent)

IWF.1: 14 residues within 4Å: Chain A: K.18, S.19, N.20, N.21, N.24, W.34, S.35, L.37, R.61, W.85, P.88, L.96, D.133 Ligands: SO4.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.88 Hydrogen bonds: A:N.20, A:N.24, A:S.35, A:R.61 Water bridges: A:D.133

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

SO4.2: 2 residues within 4Å: Chain A: R.108, E.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.109 Water bridges: A:R.108 Salt bridges: A:R.108 SO4.3: 5 residues within 4Å: Chain A: K.18, R.61, R.132, D.133 Ligands: IWF.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.133 Water bridges: A:R.61, A:R.61 Salt bridges: A:R.61, A:R.132 SO4.4: 4 residues within 4Å: Chain A: K.18, V.60, R.61, E.62 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.62 Water bridges: A:G.64, A:G.64, A:G.131 Salt bridges: A:K.18 SO4.5: 3 residues within 4Å: Chain A: S.76, H.77, H.78 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.78 Water bridges: A:H.77, A:H.77 Salt bridges: A:H.77, A:H.78

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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