Drug and Drug Target Mapping
Drugs and Drug Targets from DrugBank
Two tables provide access to information about drug and drug target information from DrugBank that are mapped to PDB entries with each weekly update. These tables, accessed from the Tools menu, can be searched, filtered, and sorted.
- Drugs Bound to Primary Targets: Lists drugs bound to primary target(s), or a homolog of primary target(s), i.e., co-crystal structures of drugs.
- Primary Drug Targets: Lists primary drug targets in the PDB, regardless if the drug molecule is part of the PDB entry (e.g., apo forms of drug targets, drug target with different bound ligands). Biotherapeutics, such as complexes with monoclonal antibodies, are included.
Search for Drugs
These tables can be limited to specific drugs by searching for a list of drugs by trade or generic names:
Drugs Bound to Primary Target Table
The table above shows the data available for the drug Acarbose, which maps to four primary drug targets (see Target Name column) based on a 30% sequence identity cutoff. Two PDB entries (2QMJ, 3TOP) match the first primary target (Malose-glucoamylase) with 99% and 97% sequence identity and contain the two stereoisomers (ACR, QPS) of acarbose. For the other three drug targets, no good drug target match could be found; the sequence identity ranges from 44% to 60%. In these cases, the proteins in these PDB entries are homologous to the primary targets.
Primary Drug Targets Only Table
The table above shows the data available for two primary drug targets of Abatacept. The first target matches the PDB entries (1NCN, 1I85), and the second target matches the PDB entry (1DR9) with 100% sequence identity. Note, there is no entry in the PDB that contains the drug Abatacept, so the table 'Drugs Bound to Primary Targets' is empty.
Description of Table Columns
|Generic name||Generic name of a drug. For approved drugs, this name is usually the WHO's International Nonproprietary Name.|
|Brand name||The name of a drug patented by a company that is used in sales.|
|DrugBank ID||Unique identifier of the drug molecule assigned by DrugBank|
|ATC codes||Anatomical Therapeutic Chemical (ATC) Classification System codes assigned by the WHO.|
|Ligand ID (for drug bound to primary target only)||3-letter code of the drug molecule in the wwPDB Chemical Component Dictionary. Any stereoisomers in the PDB that match a drug in DrugBank are listed here.|
|Target name||Drug target name from DrugBank.|
|UniProt ID||UniProt ID for the protein target sequence from DrugBank.|
|PDB ID 1 ... 3||Best three matches from the PDB that contain the drug or its stereoisomer and have >= 30% sequence identity to the primary target.|
|Sequence identity 1 ... 3||Sequence identities for the best three matches between the primary target sequence and the sequence in the PDB entries.|
|All PDB IDs||Select the word "Search" in the last column to perform a BLAST search for the primary target sequence against all sequences in the PDB with a default e-value cutoff of 10. This search produces a query results list ordered by the e-value of the BLAST search.|