SMTL ID : 8q2r.1 (1 other biounit)

Crystal structure of YTHDC1 in complex with Compound 3 (ZA_431)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

ITJ.1: 15 residues within 4Å: Chain A: K.18, S.19, N.20, N.21, N.24, W.34, S.35, T.36, W.85, V.86, P.88, M.91, L.96, D.133 Ligands: SO4.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.20, A:N.24, A:S.35, A:S.35

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

SO4.2: 4 residues within 4Å: Chain A: G.1, T.2, S.3, K.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.1, A:S.3, A:S.3, A:K.4 Water bridges: A:L.5 Salt bridges: A:K.4 SO4.3: 4 residues within 4Å: Chain A: W.122, G.134, Q.135, E.136 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.134, A:Q.135, A:E.136 Salt bridges: A:K.43 SO4.4: 3 residues within 4Å: Chain A: R.132, D.133 Ligands: ITJ.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.133 SO4.5: 2 residues within 4Å: Chain A: H.77, H.78 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.78 Salt bridges: A:H.77

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
A

YTH domain-containing protein 1

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