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

Crystal structure of YTHDC1 with compound DHU_DC1_180

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.24 Å

Oligo State

monomer

Ligands

1 x QF2: 6-[[cyclopropyl-[(7-methoxy-1,3-benzodioxol-5-yl)methyl]amino]methyl]-1~{H}-pyrimidine-2,4-dione(Non-covalent)

QF2.1: 14 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, L.104, P.105, M.108, D.150 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.51, A:W.102, A:P.105 Hydrogen bonds: A:S.52, A:L.54, A:R.78, A:R.78, A:D.150 Water bridges: A:T.53, A:N.57, A:N.57, A:D.150

6 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: 1 residues within 4Å: Chain A: K.21 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.18 Salt bridges: A:K.21 SO4.4: 5 residues within 4Å: Chain A: K.35, R.78, G.148, R.149, D.150 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:K.35, A:R.78 Salt bridges: A:K.35, A:R.78, A:R.149 SO4.5: 1 residues within 4Å: Chain A: R.125 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.125, A:R.125 Salt bridges: A:R.125 SO4.6: 3 residues within 4Å: Chain A: K.59, N.62, R.66 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.62 Water bridges: A:K.59, A:R.66, A:S.93, A:S.93 Salt bridges: A:K.59, A:R.66 SO4.7: 3 residues within 4Å: Chain A: N.38, H.39, V.77 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.39 Water bridges: A:E.40 Salt bridges: A:H.39

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

2020-07-29

Peptides

YTHDC1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

YTHDC1

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