SMTL ID : 8q4w.2 (1 other biounit)

Crystal structure of YTHDC1 in complex with Compound 40 (CS_3a)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

monomer

Ligands

1 x JNC: 5-chloranyl-3-[(3-chlorophenyl)methyl]-~{N}-methyl-2~{H}-pyrazolo[4,3-d]pyrimidin-7-amine(Non-covalent)

JNC.1: 17 residues within 4Å: Chain A: K.18, S.19, N.20, N.21, N.24, W.34, S.35, T.36, L.37, R.61, W.85, P.88, G.90, M.91, L.96, D.133 Ligands: SO4.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.37 Hydrogen bonds: A:N.20, A:N.24, A:S.35, A:D.133

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: JNC.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.133 Water bridges: A:D.133, A:D.133 Salt bridges: A:R.61 SO4.4: 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, 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 Compound 40 (CS_3a). 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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