MedChem Help

General instructions for Daylight's HTML interface to the MedChem database.

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Daylight's HTML MedChem page is a special-purpose interface to the MedChem database. It is designed to deliver essential information quickly and reliably to users who do not need to be chemical information specialists.

This interface consists of a single logical HTML page which provides for user input and display of the most commonly used database information. Hyperlinks are provided to other utilities: a graphical structure editor, raw data tabulation, live calculations, and 3-D conformation download.

Types of data available

The following types of data are available in the Medchem database:
Activity One or more general categories of pharmacological activity.
CLOGP Computed LogP(o/w), i.e., hydrophobicity as octanol/water partition coefficient.
CMR Computed molar refractivity, i.e., polarizability.
3-D Computed 3-D conformation. The medchem00 database contains 3D coordinates computed by Rubicon.
Formula Molecular formula automatically-generated from SMILES.
LogP "Raw" partition coefficient data from the literature. The Medchem database is comprehensive with respect to such data and it comprises the majority of data in the database. LogP data include reported partition coefficients measured by all methods, in all solvent pairs and of all qualities. (There are hundreds of such data for some common chemicals.)
LogP* "Preferred" value for measured partition coeffiient. Such values represent the octanol/water partition coefficient done by a high-quality method of the molecular species at 25C.
LogPgood "Good" partition coefficient value; like LogP* but doesn't meet the solvent or molecular species requirements.
Name Name of the molecule, typically a generally-accepted common name (if available). On input, all available names are accepted (spaces and case don't count). On output, the "preferred name" is reported.
pKa "Representative" acid dissociation data from the literature. Multiple pKa's are present if the molecule contains more than one acidic hydrogen.
pKa* "Preferred" value for acid dissociation constant.
WLN Wisswesser Line Notation for the molecule. WLN is an older chemical line notation not used much anymore. The Medchem database is actually keyed to WLN (nearly invisible in this interface).
CAS No. Chemical Abstracts Registry Number.

All available data are displayed except raw LogP and pKa data, which may be displayed via buttons marked "Table of raw LogP data" and "Table of raw pKa data", respectively.

Query instructions

Enter any identifier of the desired molecule in the space provided and click on the button marked "Submit". You may enter any name, CAS number, WLN, or SMILES (generic or isomeric). You may copy an entry from somewhere else and paste it into the entry field (the specific method depends on the HTML browser being used).

Alternatively, you may create or edit a structure using your choice of graphical editors, if available in your environment. These are configured by modifying the file, and if present, buttons adjacent to the input field will appear.

Report description

Data are presented below the query section on the same logical page.

Data are automatically displayed for all datatrees in the database which reference the specified identifier. Each section of output begins with a hyperlinked header: the structure (if known), the preferred name (almost always available), or the subtree identifier (e.g., WLN). Selecting a hyperlinked header re-enters MedChem with that identifier.

Data about the structure generally include Formula, CLOGP, CMR, and a conformation. The structural depiction is linked to the depict page. Hyperlinks are provided to "live" clogp and cmr calculation pages so that computational details may be examined.

Preferred names and data for each database entry follow. Buttons are provided to produce raw LogP and pKa data in tabular form (if such data are present).

Note that 3-D coordinates are not displayed directly: a button marked "Download as x-cex-3d" will appear in place of the field. When selected, the conformation will be downloaded as the "chemical/x-cex-3d" MIME type to be dispatched per your .mailcap file (typically displayed in a helper application such as rasmol). See the FAQ's for more information on setting this up.

If "black-on-paper" display is requested, depictions are drawn as black lines on a transparent background (suitable for printing on a monochrome printer).