SMTL ID : 8q2q.2 (1 other biounit)

Crystal structure of YTHDC1 in complex with Compound 2b (YL_32)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x IT6: 2-chloranyl-~{N},9-dimethyl-purin-6-amine(Non-covalent)

IT6.1: 13 residues within 4Å: Chain A: K.18, S.19, N.20, N.21, N.24, W.34, S.35, W.85, P.88, M.91, L.96, D.133 Ligands: SO4.3 3 PLIP interactions: 3 interactions with chain A 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.109 Water bridges: A:R.108, A:R.108, A:R.108, A:R.108 Salt bridges: A:R.108 SO4.3: 4 residues within 4Å: Chain A: R.61, R.132, D.133 Ligands: IT6.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.133 Water bridges: A:N.20 Salt bridges: A:R.61, A:R.132 SO4.4: 1 residues within 4Å: Chain A: K.4 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.4 Salt bridges: A:K.4 SO4.5: 3 residues within 4Å: Chain A: S.76, H.77, H.78 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.78 Salt bridges: A:H.77, A:H.78 SO4.6: 1 residues within 4Å: Chain A: K.114 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.114, A:K.114, A:K.114, A:K.114 Salt bridges: A:K.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zalesak, F. et al., Structure-Based Design of a Potent and Selective YTHDC1 Ligand. J.Med.Chem. (2024)

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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