If you are new to synPHARM we advise taking our short tutorial, with screenshots and explanations of the search functions and main features of synPHARM.
Search by Ligand
The basic Ligand Search allows you to enter a ligand's name - any ligands that at least partially match the query will be returned.
The more advanced ligand search allows for searching by essentially any combination of values that SynPharm records. This includes ligand mass, surface area, ligand type, approval status, and more.If you require a more tailored search query, you can contact us directly.
Search by Sequence
Currently searching by sequence will only return exact* matches. If you
wish to BLAST search, consider using the Guide to PHARMACOLOGY's
BLAST search feature.
*Searches will only match sequences that are stored in synPHARM, i.e. sequences extracted from PDB entries, which may often differ from the native protein sequence (e.g. the N and C termini can be truncated and sometimes residues differ or are undefined in the solved structure).
The ligands in the database are listed here, along with basic information about their approval status, GtoP type, mass, and any synonyms. This list can be sorted by any of these values (apart from synonyms), and the list can also be filtered to show only ligands of a certain type (or only approved ligands) by clicking the headers at the top of the list.
Clicking the name of any of the ligands on this list will take you to that ligand's detailed page (see below).
On the ligand's detailed page you will find more information about the ligand. This is just a subset of the information that the Guide to PHARMACOLOGY holds for the ligand - to see the full entry go to that ligand's GtoP page.
The page contains links to other databases, a structural diagram of the ligand (if available - generally peptides and antibodies do not have such images stored), and molecular information about the ligand, such as mass, surface area, and approval status. A more extensive set of database out-links for further information on the ligand is available via the GtoP page.
At the bottom of the page are links to the protein sequences which respond to this ligand.
The binding sequences in the database are listed here, along with basic information about the name of the target it is derived from, the species it is from, the ligand that binds to it, its length, and its length as a proportion of the protein chain it comes from. This list can be sorted by any of these values, and the list can also be filtered to show only sequences of a certain target type (or only sequence that respond to approved ligands) by clicking the headers at the top of the list.
Clicking the sequence ID of any of the ligands on this list will take you to that sequence's detailed page (see below).
On the left under the sequence name are links to the ligand page, and to the GtoP target page where there are out-links to other databases for further information on the target.
The sequence itself follows. The actual binding residues themselves are in bold, and the sequence can be expanded to include more of the rest of the chain using the buttons below the sequence.
Then comes the metrics about the sequence. This includes links to the PDB file the sequence was derived from, as well as certain important descriptors:
- Affinity - this is derived from the Guide to PHARMACOLOGY database, and as such are empirically determined values sourced from the literature.
- Proportional sequence length - the length of the binding sequence compared with the length of the chain it comes from. This is provided to aid the decision of whether to use the sequence itself, or simply the chain it comes from - the higher this percentage, the more useful it is to use the sequence alone.
- Contact ratio - to be useful these sequences must fold independently. Obviously this will not be the case for all the sequences here but to aid in judging how likely they are to do so, the ratio of internal contacts (atomic distances less than five Angstroms within the sequence) to external contacts (atomic distances between the sequence and the rest of the chain less than five Angstroms) is provided. This represents the degree to which the sequence is 'self-contained' - the higher this ratio, the more 'domain-like' the sequence is and the more likely it is believed to be able to fold independently.
Below this is a feature viewer, which shows the location of binding residues and secondary structure elements along the sequence, as well as measures of hydrophobicity along the sequence.
Finally, there is a residue distance matrix for the whole chain, with the binding sequence itself marked as a dotted line. This graphic shows the distance between any two given residues, with green representing nearby residues and red distant residues (capped at 40 Angstroms). This is provided to give a sense of how 'globular' a binding sequence is within its chain of origin - if the area within the dotted line is much greener than the surrounding area, it is a compact sequence.
(Note that some areas of the matrix will be white - this is because some residues in that chain are missing from the PDB file of origin, and so there is no location information available.)
This resource is maintained by the Guide to PHARMACOLOGY team. To contact a member of the team, use the e-mail address here and indicate that your enquiry concerns SynPharm in the subject line.