SMTL ID : 7r5l.1

Crystal structure of YTHDF2 with compound YLI_DC1_015

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x I4S: 3,6-dimethyl-2~{H}-1,2,4-triazin-5-one(Non-covalent)

I4S.1: 12 residues within 4Å: Chain A: K.31, S.32, Y.33, D.37, W.47, C.48, S.49, T.50, W.101, W.106, D.143 Ligands: SO4.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.47, A:T.50, A:W.101 Hydrogen bonds: A:Y.33, A:C.48 Water bridges: A:D.37, A:S.102

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

SO4.2: 6 residues within 4Å: Chain A: K.31, Y.33, N.77, R.142, D.143 Ligands: I4S.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.77, A:D.143 Water bridges: A:R.142, A:R.142, A:R.142 Salt bridges: A:R.142 SO4.3: 3 residues within 4Å: Chain A: R.40, K.43, Y.44 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.40, A:K.43 SO4.4: 5 residues within 4Å: Chain A: N.122, R.126, T.139, N.140 Ligands: SO4.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.122, A:T.139 Salt bridges: A:R.126 SO4.5: 12 residues within 4Å: Chain A: K.31, S.75, V.76, N.77, G.78, S.79, G.80, H.81, N.122, T.139 Ligands: SO4.4, SO4.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.78, A:S.79, A:G.80, A:H.81, A:N.122 Water bridges: A:S.75 Salt bridges: A:K.31 SO4.6: 4 residues within 4Å: Chain A: K.31, N.77, G.78 Ligands: SO4.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.77, A:G.78 Water bridges: A:K.31, A:R.142 Salt bridges: A:K.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nai, F. et al., Fragment Ligands of the m 6 A-RNA Reader YTHDF2. Acs Med.Chem.Lett. (2022)

Release Date

2022-03-02

Peptides

YTH domain-containing family protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

YTH domain-containing family protein 2

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