SMTL ID : 6ynj.1 (1 other biounit)

Crystal structure of YTHDC1 with compound DHU_DC1_046

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

2 x P0N: (2~{R})-2-(2-chlorophenyl)-5,5-dimethyl-morpholine(Non-covalent)

P0N.1: 11 residues within 4Å: Chain A: N.41, W.51, S.52, L.54, W.102, P.105, M.108, S.109, M.112, L.113 Ligands: SO4.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.41, A:W.51, A:L.54, A:W.102, A:W.102, A:M.108, A:M.112, A:L.113, A:L.113 Hydrogen bonds: A:S.52 P0N.2: 3 residues within 4Å: Chain A: P.138, W.139, H.142 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.138, A:W.139, A:W.139 Water bridges: A:E.155

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

SO4.3: 4 residues within 4Å: Chain A: K.60, W.139, Q.152, E.153 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.152, A:Q.152, A:E.153 Water bridges: A:K.60, A:K.60, A:E.153 Salt bridges: A:K.60 SO4.4: 2 residues within 4Å: Chain A: H.94, H.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.95 Salt bridges: A:H.94 SO4.5: 7 residues within 4Å: Chain A: S.36, N.37, N.38, N.41, W.51, R.78 Ligands: P0N.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.36, A:N.37, A:N.37, A:N.38, A:N.41, A:R.78

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
A

YTHDC1

Related Entries With Identical Sequence