SMTL ID : 8q4v.1 (1 other biounit)

Crystal structure of YTHDC1 in complex with Compound 37 (ZA_356)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

monomer

Ligands

1 x JO0: 2-chloranyl-9-[(3-chlorophenyl)methyl]-~{N}-cyclopropyl-7,8-dihydropurin-6-amine(Non-covalent)

JO0.1: 13 residues within 4Å: Chain A: K.18, S.19, N.20, N.21, N.24, W.34, S.35, W.85, V.86, P.88, L.96, D.133 Ligands: SO4.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.85, A:W.85, A:L.96 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.1, A:S.3, A:S.3, A:K.4 Water bridges: A:L.5 Salt bridges: A:K.4 SO4.3: 5 residues within 4Å: Chain A: K.43, W.122, G.134, Q.135, E.136 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.134, A:Q.135, A:E.136 Water bridges: A:W.122 Salt bridges: A:K.43 SO4.4: 2 residues within 4Å: Chain A: 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 SO4.5: 3 residues within 4Å: Chain A: R.132, D.133 Ligands: JO0.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.133 Water bridges: A:N.40

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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