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

Crystal structure of YTHDC1 with compound VVR_DC1_002

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x P5H: 6-methyl-~{N}-[2-(methylsulfonylamino)ethyl]-2-oxidanylidene-3~{H}-pyridine-3-carboxamide(Non-covalent)

P5H.1: 14 residues within 4Å: Chain A: K.35, S.36, N.37, N.41, W.51, S.52, T.53, L.54, W.102, L.104, M.108, L.113, D.150 Ligands: SO4.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.102, A:L.104 Hydrogen bonds: A:N.37, A:D.150

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

SO4.2: 2 residues within 4Å: Chain A: R.125, E.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.126 Water bridges: A:R.125 Salt bridges: A:R.125 SO4.3: 2 residues within 4Å: Chain A: G.18, K.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.18 Salt bridges: A:K.21 SO4.4: 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:H.95 Salt bridges: A:H.94, A:H.95 SO4.5: 3 residues within 4Å: Chain A: R.149, D.150 Ligands: P5H.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.150

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

Related Entries With Identical Sequence