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

Crystal structure of YTHDC1 with compound DHU_DC1_234

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

1 x OW8: ~{N}-methyl-1,4,5,6-tetrahydrocyclopenta[c]pyrazole-3-carboxamide(Non-covalent)

OW8.1: 11 residues within 4Å: Chain A: N.37, N.41, W.51, S.52, T.53, L.54, W.102, P.105, M.108, L.113, D.150 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.54, A:P.105 Hydrogen bonds: A:N.41, A:S.52, A:T.53, A:T.53, A:L.54, A:D.150

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

SO4.2: 4 residues within 4Å: Chain A: G.18, T.19, S.20, K.21 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.18, A:S.20, A:K.21 Water bridges: A:G.18, A:G.18, A:G.18, A:T.19, A:T.19, A:S.20, A:K.21 Salt bridges: A:K.21 SO4.3: 4 residues within 4Å: Chain A: K.60, W.139, Q.152, E.153 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.152, A:E.153 Water bridges: A:Q.152, A:Q.152 Salt bridges: A:K.60 SO4.4: 3 residues within 4Å: Chain A: R.78, R.149, D.150 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:R.78, A:R.78, A:R.78, A:R.78, A:D.150 Salt bridges: A:R.78 SO4.5: 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

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

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