Package name: (5S)-5-(1H-indol-3-ylmethyl)imidazolidine-2,4-dione

Package ID: 2928
Force-field: OPLS-AA | Code: Gromacs
Created by Oliver Beckstein (oliver)
Created at 2016-11-17 21:16:36
Modified at 2016-11-17 21:16:36

Abstract

OPLS-AA parameters for L-indolylmethyl-hydantoin, the preferred substrate for the sodium-coupled nucleobase symporter Mhp1.

Chemical structure
General view

 Detailed view

References
Authors: K. J. Simmons, S. M. Jackson, F. Bru ̈ckner, S. G. Patching, O. Beckstein, E. Ivanova, T. Geng, S. Weyand, D. Drew, J. Lannigan, D. J. Sharples, M. S. P. Sansom, S. Iwata, C. W. Fishwick, A. P. Johnson, A. D. Cameron, and P. J. Henderson
Title: Molecular mechanism of ligand recognition by membrane transport protein, Mhp1
Journal: EMBO J
Year: 2014
Volume: 33
Pages: 1831-1844
DOI: 10.15252/embj.201387557
Pubmed ID:   24952894
Comments:

Reference validation values

These are experimental values or high-level quantum mechanics values, which will be used for comparison with computed values (found in individual versions).

Files and history

All deposited versions are available and can be downloaded individually. Higher version numbers are more recent. Files that changed between versions can be identified by differing SHA1 hash checksums.

Version 1 created at 2016-11-17

Score 2/5 "Reasonable parameterization based on analogy but no direct validation data available. Preferred bound conformation in Mhp1 is same rotamer in X-ray structure and simulations (extended conformation)."

Computed validation values

grompp
preprocessor output "grompp-compatible"
Created at 2016-11-17 21:16:36 | Modified at 2016-11-17 21:16:36 | [download zip]
Type Description Hash (SHA1)
Topology indolylmethylhyd5.itp baff20ad4848bb887a168b269140c6a0a6f8502a
Structure indolylmethylhyd5.pdb d8f589735a97033f946882a7f02532b54f6b5a95

Compound details
Ligand code I5H
Molecule identifier B902A10D19EFE466
Displayed name (5S)-5-(1H-indol-3-ylmethyl)imidazolidine-2,4-dione
Canonical IUPAC name (5S)-5-(1H-indol-3-ylmethyl)imidazolidine-2,4-dione
Formula C12H11N3O2
Molecular weight 229.24
Charge 0
Number of atoms 28
SMILES N1C(=O)NC([C@@H]1CC2=C[NH]C3=C2C=CC=C3)=O
PubChem CID 1550957
CAS RN 40856-80-2
Other names (5S)-5-(1H-indol-3-ylmethyl)imidazolidine-2,4-dione • (5S)-5-(1H-indol-3-ylmethyl)hydantoin • ZINC01682922

License
Type CC BY-SA – Creative Commons Attribution-Share Alike License
Name Oliver Beckstein
Email (hidden)
Source mol2ff (Bogdan Iorga)

Ligandbook is described in

Jan Domański, Oliver Beckstein, Bogdan I. Iorga; Ligandbook: an online repository for small and drug-like molecule force field parameters, Bioinformatics, Volume 33, Issue 11, 1 June 2017, Pages 1747–1749, https://doi.org/10.1093/bioinformatics/btx037

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