SMTL ID : 8q4n.1 (1 other biounit)

Crystal structure of YTHDC1 in complex with Compound 26 (ZA_513)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

monomer

Ligands

1 x JIR: 3-[[2-chloranyl-6-(methylamino)purin-9-yl]methyl]benzenecarbonitrile(Non-covalent)

JIR.1: 14 residues within 4Å: Chain A: K.18, S.19, N.20, N.21, N.24, W.34, S.35, L.37, W.85, V.86, P.88, L.96, D.133 Ligands: SO4.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.37 Hydrogen bonds: A:N.20, A:N.24, A:S.35 Halogen bonds: A:N.21

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

SO4.2: 4 residues within 4Å: Chain A: G.1, T.2, S.3, K.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.1, A:S.3, A:K.4 Salt bridges: A:K.4 SO4.3: 3 residues within 4Å: Chain A: N.20, P.88, A.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.20, A:A.89 SO4.4: 6 residues within 4Å: Chain A: K.18, R.61, G.131, R.132, D.133 Ligands: JIR.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.131, A:D.133 Salt bridges: A:R.61 SO4.5: 2 residues within 4Å: Chain A: H.77, H.78 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.78 Salt bridges: A:H.77

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
A

YTH domain-containing protein 1

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