SMTL ID : 8q4r.2 (1 other biounit)

Crystal structure of YTHDC1 in complex with Compound 30 (ZA_326)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

monomer

Ligands

1 x JHU: [4-[[2-chloranyl-6-(methylamino)purin-9-yl]methyl]phenyl]methanol(Non-covalent)

JHU.1: 15 residues within 4Å: Chain A: K.18, S.19, N.20, N.21, N.24, W.34, S.35, L.37, W.85, P.88, G.90, M.91, L.96, D.133 Ligands: SO4.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.37, A:L.37, A:P.88 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: 2 residues within 4Å: Chain A: R.108, E.109 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.109 Salt bridges: A:R.108 SO4.3: 4 residues within 4Å: Chain A: R.61, R.132, D.133 Ligands: JHU.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.133 Salt bridges: A:R.61, A:R.132 SO4.4: 2 residues within 4Å: Chain A: R.108, P.150 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bedi, R.K. et al., Crystal structure of YTHDC1 in complex with Compound 30 (ZA_326). To Be Published

Release Date

2023-12-06

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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