SMTL ID : 6yni.2 (1 other biounit)

Crystal structure of YTHDC1 with compound DHU_DC1_036

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

monomer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: S.36, N.37, N.38, N.41, W.51 Ligands: P0Q.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.36, A:N.37, A:N.38, A:N.41, A:R.78 SO4.2: 2 residues within 4Å: Chain A: R.125, E.126 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.126 Water bridges: A:R.125, A:R.125 Salt bridges: A:R.125 SO4.3: 3 residues within 4Å: Chain A: S.93, H.94, H.95 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.95 Water bridges: A:S.93, A:S.93 Salt bridges: A:H.94 SO4.4: 3 residues within 4Å: Chain A: R.78, R.149, D.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.150 Salt bridges: A:R.78, A:R.149 SO4.5: 3 residues within 4Å: Chain A: K.35, R.78, E.79 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.79 Water bridges: A:G.148 Salt bridges: A:K.35 SO4.6: 5 residues within 4Å: Chain A: F.65, S.90, S.91, E.92, H.94 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.92, A:E.92 Salt bridges: A:H.94

2 x P0Q: (2~{R},3~{R})-2-(3-chlorophenyl)-3,5,5-trimethyl-morpholine(Non-covalent)

P0Q.7: 13 residues within 4Å: Chain A: N.41, W.51, S.52, L.54, W.102, V.103, L.104, P.105, M.108, S.109, M.112, L.113 Ligands: SO4.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:N.41, A:W.51, A:W.102, A:W.102, A:P.105 Halogen bonds: A:S.109 P0Q.8: 2 residues within 4Å: Chain A: H.101, W.102 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:H.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Structure-based design of ligands of the m6A-RNA reader YTHDC1. Eur J Med Chem Rep (2022)

Release Date

2020-07-15

Peptides

YTHDC1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

YTHDC1

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