6t0a | pdb_00006t0a

Crystal structure of YTHDC1 with fragment 25 (PSI_DC1_005)

spinqualitylabelsall models 6t0a, resolution 2.02Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6t0a is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: M58, SO4 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [YTDC1_HUMAN] RNA-binding protein that regulates alternative splice site selection. Publication Abstract from PubMed We report a crystallographic analysis of small-molecule ligands of the human YTHDC1 domain that recognizes N6-methylated adenine (m(6)A) in RNA. The 30 binders are fragments (molecular weight < 300 g mol(-1)) that represent 10 different chemotypes identified by virtual screening. Despite the structural disorder of the binding site loop (residues 429-439), most of the 30 fragments emulate the two main interactions of the -NHCH3 group of m(6)A. These interactions are the hydrogen bond to the backbone carbonyl of Ser378 and the van der Waals contacts with the tryptophan cage. Different chemical groups are involved in the conserved binding motifs. Some of the fragments show favorable ligand efficiency for YTHDC1 and selectivity against other m(6)A reader domains. The structural information is useful for the design of modulators of m(6)A recognition by YTHDC1. Selectively Disrupting m(6)A-Dependent Protein-RNA Interactions with Fragments.,Bedi RK, Huang D, Wiedmer L, Li Y, Dolbois A, Wojdyla JA, Sharpe ME, Caflisch A, Sledz P ACS Chem Biol. 2020 Mar 2. doi: 10.1021/acschembio.9b00894. PMID:32101404 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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