SMTL ID : 8q33.1 (1 other biounit)

Crystal structure of YTHDC1 in complex with Compound 15 (ZA_343)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

monomer

Ligands

1 x IWV: ~{N}-[2-[[2-chloranyl-6-(methylamino)purin-9-yl]methyl]phenyl]-2,2,2-tris(fluoranyl)ethanamide(Non-covalent)

IWV.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, V.86, P.88, L.96, D.133 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

5 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: 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 SO4.5: 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 SO4.6: 3 residues within 4Å: Chain A: S.76, 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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