Article Figures & Data
Figures
- Figure 1
Statistics of three-dimensional (3D) protein structures in Protein Data Bank (PDB; December,2019). (A) 3D protein structures distributed in different species. (B) 3D protein structures parsed by different methods. (C) The resolution of 3D protein structures in PDB. (D) Increasing trend of published 3D protein structures during last two decades. NMR, nuclear magnetic resonance.
- Figure 2
Three-dimensional (3D) protein structural alignment of VISTA (crystal structure) and homologous reconstructed model. (A) VISTA crystal structure (6oil, resolution=1.85 Å). (B) VISTA model. (C) 3D structural alignment between real 3D structure and 3D model (root mean SD=3.6 Å).
- Figure 3
Identification of polymerisation pocket on gasdermin D (GSDMD) by 3D protein structural alignment. (A) Human GSDMD (6n9o). (B) Mouse GSDMD (6n9n), red amino acid residues are verified polymerisation-associated residues. (C) 3D alignment for the identification of corresponding polymerisation pocket residues on human GSDMD.
- Figure 4
Identification of allosteric pocket on mutant p53. (A) Three-dimensional (3D) structural alignment of 43 p53 DNA binding domain. (B) DNA binding pocket is composed of fluctuating coli structures (double helix structure represents DNA). (C) Allosteric pocket (red amino acid residues) on p53(4lof) predicted by molecular dynamic simulation and hot spot mutant residues (purple).
Tables
- Table 1
Protein structure databases
Database URL Description Therapeutic Target Database (TTD) https://db.idrblab.org/ttd/ Known potential therapeutic targets, including protein and nucleic acid targets, were collected from the existing literature. However, the 3D structures of many of these targets have not yet been resolved. Potential Drug-Target Database (PDTD) http://www.dddc.ac.cn/pdtd/ Similar to TTD, PDTD contains only protein receptors and is a protein receptor with a known 3D structure. Drug Adverse Reaction Database (DART) http://bidd.nus.edu.sg/group/drt This is for protein receptors that have adverse drug reactions Small Molecule Transcription Factor Database (SM-TF) http://zoulab.dalton.missouri.edu/SM-TF/ The structures of transcription factors that bind to small molecules are collected from the Protein Data Bank (PDB). The dysfunction of transcription factors is directly related to many diseases and is the target protein of many drugs. PDBbind (a comprehensive collection of binding affinities for the protein–ligand complexes in the PDB) WWW.pdbbind.org.cn All protein–ligand complex structures with experimentally measured binding affinity data in the PDB database were collected. In addition to experimental binding affinity data (Kd, Ki or IC50), the database also provides the cleaned protein 3D structure and corresponding ligand structure. 3D, three-dimensional; IC50, half maximal (50%) inhibitory concentration of a substance.
