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

Crystal structure of YTHDC1 with compound DHU_DC1_135

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

1 x P0B: 6-[[(2-chloranyl-6-fluoranyl-phenyl)methyl-methyl-amino]methyl]-1~{H}-pyrimidine-2,4-dione(Non-covalent)

P0B.1: 16 residues within 4Å: Chain A: K.35, S.36, N.37, N.41, W.51, S.52, T.53, L.54, R.78, W.102, V.103, L.104, P.105, M.108, L.113, D.150 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.54, A:L.104, A:P.105 Hydrogen bonds: A:N.37, A:S.52, A:R.78, A:R.78, A:D.150 Water bridges: A:N.57, A:D.150, A:D.150 Halogen bonds: A:V.103

5 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.18 Water bridges: A:G.18, A:G.18, A:K.21, A:K.21, A:K.21 Salt bridges: A:K.21 SO4.4: 1 residues within 4Å: Chain A: R.125 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.125, A:R.125, A:R.125, A:R.125, A:E.170 Salt bridges: A:R.125 SO4.5: 4 residues within 4Å: Chain A: K.35, R.78, R.149, D.150 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:K.35, A:K.35, A:R.149, A:R.149 Salt bridges: A:K.35, A:R.78, A:R.149 SO4.6: 3 residues within 4Å: Chain A: K.59, N.62, R.66 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.62 Water bridges: A:K.59, A:K.59, A:R.66 Salt bridges: A:K.59, A:R.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Atomistic and Thermodynamic Analysis of N6-Methyladenosine (m 6 A) Recognition by the Reader Domain of YTHDC1. J Chem Theory Comput (2021)

Release Date

2020-07-15

Peptides

YTHDC1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

YTHDC1

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