SMTL ID : 8q4n.2 (1 other biounit)

Crystal structure of YTHDC1 in complex with Compound 26 (ZA_513)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

monomer

Ligands

1 x JIR: 3-[[2-chloranyl-6-(methylamino)purin-9-yl]methyl]benzenecarbonitrile(Non-covalent)

JIR.1: 14 residues within 4Å: Chain A: K.18, S.19, N.20, N.21, N.24, W.34, S.35, T.36, L.37, W.85, P.88, L.96, D.133 Ligands: SO4.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.37 Hydrogen bonds: A:N.20, A:N.24, A:S.35

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

SO4.2: 2 residues within 4Å: Chain A: R.108, E.109 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.109 Water bridges: A:R.108, A:R.108 Salt bridges: A:R.108 SO4.3: 1 residues within 4Å: Chain A: K.4 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.4 SO4.4: 1 residues within 4Å: Chain A: R.108 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.108 SO4.5: 4 residues within 4Å: Chain A: R.61, R.132, D.133 Ligands: JIR.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.133 Water bridges: A:N.40, A:D.133, A:D.133, A:D.133 Salt bridges: A:R.61 SO4.6: 4 residues within 4Å: Chain A: K.18, V.60, R.61, E.62 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.61, A:E.62 Water bridges: A:G.131 Salt bridges: A:K.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bedi, R.K. et al., Crystal structure of YTHDC1 in complex with Compound 26 (ZA_513). 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

Related Entries With Identical Sequence