SMTL ID : 9h2t.1 (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: 14 residues within 4Å: Chain A: K.18, N.20, N.24, W.34, S.35, T.36, L.37, R.61, W.85, P.88, M.91, L.96, D.133 Ligands: SO4.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.34, A:L.37, A:W.85, A:W.85, A:L.96, A:D.133 Hydrogen bonds: A:N.20, A:L.37

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

SO4.2: 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 SO4.3: 3 residues within 4Å: Chain A: K.18, R.61, E.62 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.62 Water bridges: A:K.18, A:K.18, A:K.18, A:G.131 Salt bridges: A:K.18, A:R.61 SO4.4: 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 SO4.5: 4 residues within 4Å: Chain A: G.1, T.2, S.3, K.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.1, A:S.3, A:K.4 Water bridges: A:T.2, A:S.3, A:L.5 Salt bridges: A:K.4 SO4.6: 3 residues within 4Å: Chain A: S.76, H.77, H.78 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.78 Water bridges: A:H.78 Salt bridges: A:H.77, A:H.78

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
A

YTH domain-containing protein 1

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