SMTL ID : 8q2s.1 (1 other biounit)

Crystal structure of YTHDC1 in complex with Compound 4 (ZA_232)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

monomer

Ligands

1 x IU2: 2-chloranyl-~{N}-methyl-9-phenyl-purin-6-amine(Non-covalent)

IU2.1: 13 residues within 4Å: Chain A: K.18, S.19, N.20, N.21, N.24, W.34, S.35, T.36, W.85, V.86, P.88, L.96, D.133 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.18, A:D.133 Hydrogen bonds: A:N.20, A:N.24, A:S.35 Halogen bonds: A:N.21

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

SO4.2: 4 residues within 4Å: Chain A: G.1, T.2, S.3, K.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.1, A:S.3, A:S.3, A:K.4 Water bridges: A:S.3, A:S.3, A:K.4, A:K.4, A:L.5 Salt bridges: A:K.4 SO4.3: 4 residues within 4Å: Chain A: K.43, W.122, 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 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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