SMTL ID : 9h2t.2 (1 other biounit)

Crystal structure of YTHDC1 in complex with AI_04

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.31 Å

Oligo State

monomer

Ligands

1 x 01: 6-cyclopropyl-3-phenyl-1~{H}-pyrimidine-2,4-dione

01.1: 15 residues within 4Å: Chain A: K.18, N.20, N.24, W.34, S.35, T.36, L.37, R.61, W.85, L.87, P.88, M.91, L.96, D.133 Ligands: SO4.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.34, A:L.37, A:W.85, A:L.87, A:L.96, A:D.133 Hydrogen bonds: A:N.20, A:L.37

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

SO4.2: 2 residues within 4Å: Chain A: R.108, E.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.109 Water bridges: A:R.108 Salt bridges: A:R.108 SO4.3: 4 residues within 4Å: Chain A: R.61, R.132, D.133 Ligands: 01.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.133 Water bridges: A:R.61, A:R.61, A:D.133 Salt bridges: A:R.61 SO4.4: 1 residues within 4Å: Chain A: R.108 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.108, A:R.108 Salt bridges: A:R.108 SO4.5: 3 residues within 4Å: Chain A: N.20, P.88, A.89 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.20, A:A.89 Water bridges: A:N.20, A:N.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bedi, R.K. et al., Crystal structure of YTHDC1 in complex with AI_04. To Be Published

Release Date

2025-08-27

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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