NMRFAM Logo BMOD logo

Biomolecular Modeling Database (BMOD)

Search:

5-(Hydroxymethyl)Uracil (C5H6N2O3)

  • Cite this entry: PDF Text

  • Download entry: Compressed file
  • InChI: InChI=1S/C5H6N2O3/c8-2-3-1-6-5(10)7-4(3)9/h1,8H,2H2,(H2,6,7,9,10)
  • SMILES: O=c1[nH]cc(CO)c(=O)[nH]1
  • NMR-STAR: BMOD0000000408.str
  • Compound details: BMRB metabolite

Graphical representations:

Image for 5-(Hydroxymethyl)Uracil

Molecular modeling parameter files

RUNER (Download)

Xplor-NIH (Download)

AMBER (Download)

CHARMM (Download)

Reference citations:

  • Dashti Hesam, Westler William M., Markley John L., Eghbalnia Hamid R., Unique identifiers for small molecules enable rigorous labeling of their atoms, Scientific Data, 2017, 4, ., doi:10.1038/sdata.2017.73, https://www.nature.com/articles/sdata201773

  • Dashti Hesam, Wedell Jonathan R., Cornilescu Gabriel, Schwieters Charles D., Westler William M., Markley John L., Eghbalnia Hamid R., Robust nomenclature and software for enhanced reproducibility in molecular modeling of small molecules, biorxiv preprint, 2018, ., ., https://doi.org/10.1101/429530, https://www.biorxiv.org/content/early/2018/09/27/429530

  • Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL., BioMagResBank, Nucleic Acids Res., 2008 Jan, 36, Database, doi:10.1093/nar/gkm957

  • Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA., Development and testing of a general amber force field., J. Comput Chem., 2004 Jul, 25, 9, doi: 0.1002/jcc.20035

  • Wang Junmei, Wang Wei, Kollman Peter A., Case David A., Automatic atom type and bond type perception in molecular mechanical calculations., Journal of Molecular Graphics and Modelling, 2006, 25, 2, https://doi.org/10.1016/j.jmgm.2005.12.005

  • TopSpin V.4, Bruker; https://www.bruker.com/products/mr/nmr/nmr-software/nmr-software/topspin/overview.html

  • Thain Douglas, Tannenbaum Todd, Livny Miron , Distributed computing in practice: the Condor experience, CONCURRENCY AND COMPUTATION: PRACTICE AND EXPERIENCE, 2005, 17, ., DOI:10.1002/cpe.938

  • RDKit: Open-source cheminformatics; http://www.rdkit.org
Disclaimer:
  • BMOD is available to the public as a web-service via our web server. This work is copyrighted under the terms of GPL. The data entries are provided on an "as is" basis without warranty of any kind, either expressed or implied. Any usage of BMOD data entries, or modification and application of the data are free for academic use when BMOD publications are cited.
  • The chemical compounds archived in this database are aggregated from several different databases and have been processed with different software packages. For appropriate citation of the data entries please check the PDF description files provided for every entry.
  • The majority of the aggregated compounds are provided in 2D structure and with implicit hydrogen atoms. We utilized the Open Babel (The Open Source Chemistry Toolbox) software package to add explicit hydrogen atoms and to generate 3D structure of the compounds; please comply with the Open Babel license agreements.
Contact:
    For any question or concern please contact Hesam Dashti (hdashti@bwh.harvard.edu).
Flag Counter