SMTL ID : 8q2u.2 (1 other biounit)

Crystal structure of YTHDC1 in complex with Compound 6 (ZA_308)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

monomer

Ligands

1 x IUH: 2-chloranyl-~{N}-methyl-9-(pyridin-4-ylmethyl)purin-6-amine(Non-covalent)

IUH.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, M.91, L.96, D.133 Ligands: SO4.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.20, A:N.24, A:S.35 Halogen bonds: A:N.21

5 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: 2 residues within 4Å: Chain A: R.61, E.62 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.62 Water bridges: A:R.61, A:R.61 Salt bridges: A:K.18, A:R.61 SO4.4: 3 residues within 4Å: Chain A: K.42, N.45, R.49 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.45 Salt bridges: A:R.49 SO4.5: 4 residues within 4Å: Chain A: R.61, R.132, D.133 Ligands: IUH.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 SO4.6: 3 residues within 4Å: Chain A: S.76, H.77, H.78 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.78 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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