SMTL ID : 8q2s.2 (1 other biounit)

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

Coordinates

PDB Format

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: 14 residues within 4Å: Chain A: K.18, S.19, N.20, N.21, N.24, W.34, S.35, T.36, W.85, P.88, M.91, L.96, D.133 Ligands: SO4.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.133 Hydrogen bonds: A:N.20, A:N.24, A:S.35

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

SO4.2: 2 residues within 4Å: Chain A: R.108, E.109 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.109 Water bridges: A:R.108, A:R.108, A:R.108 Salt bridges: A:R.108 SO4.3: 1 residues within 4Å: Chain A: R.108 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.108 SO4.4: 3 residues within 4Å: Chain A: R.132, D.133 Ligands: IU2.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.133 Water bridges: A:D.133, A:D.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bedi, R.K. et al., Crystal structure of YTHDC1 in complex with Compound 4 (ZA_232). 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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