title: Small molecule annotation for the Protein Data Bank.
abstract: The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100,000 structures contain more than 20,000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors.
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan ssen@ebi.ac.uk.
authors.forename: Sanchayita
authors.initials: S
authors.lastname: Sen
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Jasmine
authors.initials: J
authors.lastname: Young
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: John M
authors.initials: JM
authors.lastname: Berrisford
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Minyu
authors.initials: M
authors.lastname: Chen
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Conroy
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Shuchismita
authors.initials: S
authors.lastname: Dutta
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Luigi
authors.initials: L
authors.lastname: Di Costanzo
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Guanghua
authors.initials: G
authors.lastname: Gao
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Sutapa
authors.initials: S
authors.lastname: Ghosh
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Brian P
authors.initials: BP
authors.lastname: Hudson
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Reiko
authors.initials: R
authors.lastname: Igarashi
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Yumiko
authors.initials: Y
authors.lastname: Kengaku
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Yuhe
authors.initials: Y
authors.lastname: Liang
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Ezra
authors.initials: E
authors.lastname: Peisach
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Irina
authors.initials: I
authors.lastname: Persikova
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Abhik
authors.initials: A
authors.lastname: Mukhopadhyay
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Buvaneswari Coimbatore
authors.initials: BC
authors.lastname: Narayanan
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Gaurav
authors.initials: G
authors.lastname: Sahni
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Junko
authors.initials: J
authors.lastname: Sato
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Monica
authors.initials: M
authors.lastname: Sekharan
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Chenghua
authors.initials: C
authors.lastname: Shao
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Lihua
authors.initials: L
authors.lastname: Tan
authors.affiliation: Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
authors.forename: Marina A
authors.initials: MA
authors.lastname: Zhuravleva
mesh_terms: D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000494:pharmacology; D001665:Binding Sites; D057225:Data Mining; D062126:Databases, Chemical; D030562:Databases, Protein; D005947:Glucose / Q000737:chemistry; D006020:Glycopeptides / Q000737:chemistry / Q000494:pharmacology; D008024:Ligands; D008958:Models, Molecular; D015203:Reproducibility of Results; D054852:Small Molecule Libraries / Q000737:chemistry* / Q000494:pharmacology
chemical_list: D000900:Anti-Bacterial Agents; D006020:Glycopeptides; D008024:Ligands; D054852:Small Molecule Libraries; D005947:Glucose