SMTL ID : 8q4u.1 (1 other biounit)

Crystal structure of YTHDC1 in complex with Compound 36 (ZA_540b)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

monomer

Ligands

1 x JA0: 9-[(3-chlorophenyl)methyl]-2-fluoranyl-~{N}-methyl-purin-6-amine(Non-covalent)

JA0.1: 13 residues within 4Å: Chain A: K.18, S.19, N.20, N.21, N.24, W.34, S.35, L.37, W.85, P.88, M.91, L.96, D.133 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.37 Hydrogen bonds: A:N.20, A:N.24, A:S.35 Halogen bonds: A:N.21

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

SO4.2: 4 residues within 4Å: Chain A: G.1, T.2, S.3, K.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.1, A:S.3, A:S.3, A:K.4 Water bridges: A:L.5 Salt bridges: A:K.4 SO4.3: 5 residues within 4Å: Chain A: K.43, W.122, G.134, Q.135, E.136 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.134, A:Q.135, A:E.136 Water bridges: A:W.122 Salt bridges: A:K.43 SO4.4: 3 residues within 4Å: Chain A: N.20, P.88, A.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.20, A:A.89 SO4.5: 2 residues within 4Å: Chain A: H.77, H.78 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.78, A:H.78 Salt bridges: A:H.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bedi, R.K. et al., Crystal structure of YTHDC1 in complex with Compound 36 (ZA_540b). To Be Published

Release Date

2023-12-06

Peptides

YTH domain-containing protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

YTH domain-containing protein 1

Related Entries With Identical Sequence