SMTL ID : 9h2u.1 (1 other biounit)

Crystal structure of YTHDC1 in complex with AI_033

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.21 Å

Oligo State

monomer

Ligands

3 x WPS: 5-amino-3-methyl-1H-pyrazole-4-carbonitrile(Non-covalent)

WPS.1: 12 residues within 4Å: Chain A: K.18, S.19, N.20, N.24, W.34, S.35, T.36, W.85, L.87, P.88, M.91, D.133 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.34, A:W.34, A:W.85, A:L.87 Hydrogen bonds: A:N.20, A:N.24, A:T.36, A:T.36, A:D.133 Water bridges: A:R.61 WPS.2: 6 residues within 4Å: Chain A: L.9, Q.10, D.11, L.139, E.140, T.143 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.139, A:L.139 Hydrogen bonds: A:L.9, A:L.9, A:Q.10, A:D.11 Water bridges: A:Q.144 WPS.3: 6 residues within 4Å: Chain A: V.33, G.80, S.81, I.83, V.99, K.101 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.33 Hydrogen bonds: A:S.81 Water bridges: A:H.77, A:G.80, A:V.99

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

SO4.4: 4 residues within 4Å: Chain A: G.1, T.2, S.3, K.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.1, A:G.1, A:S.3, A:K.4 Water bridges: A:K.4, A:K.4 Salt bridges: A:K.4 SO4.5: 3 residues within 4Å: Chain A: R.61, R.132, D.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.133 Water bridges: A:D.133 Salt bridges: A:R.61 SO4.6: 2 residues within 4Å: Chain A: 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 AI_033. To Be Published

Release Date

2025-08-27

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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