Cambridge Structural Database (CSD) is a worldwide repository of small molecule crystal structures hosted by Cambridge Crystallographic Data Center (CCDC). The latest release is 2022.1 (Mar 2022). The 2022.1 CSD Release contains over 1,156,000 unique structures and 1,181,000 entries.
To stay up-to-date with the latest releases, check the CCDC page What's New
The University of Michigan has an unlimited site license to access CSD. You may access the database via either of the following two means.
2. Install Cambridge Structural Database (CSD) on your own computer.
Note: Every new release requires a complete re-installation of the software and data.
The installation takes 3 steps: files download, installation, and entering the license information.
Step 1. File Download
Request the software download links directly from CCDC: http://www.ccdc.cam.ac.uk/support-and-resources/csdsdownloads/. You will need our site number and confirmation code, and your email@example.com email address. Once you submit the request successfully, an email with the download links will be sent to you. (Be sure to check your Spam folder. It may take some time for the email to be sent, it is not immediate. Please allow for up to an hour.) Follow the links and instructions in the email to download and install the software appropriate to your operating system. Please contact the Chemistry Librarian if you encounter an error message.
Step 2. Install the Software
Run the installer
Optional, if prefer using the command line: https://www.ccdc.cam.ac.uk/sup
Step 3. Enter License Information
Since we recently installed the license server, two options to configure the new install are available to you:
Different operating systems:
If you are running on Windows or Linux, you should be able to install the latest updates seamlessly by simply clicking on Help > Check for Updates in either Mercury or Hermes. If you experience any problems, or you are running on Mac OSX, you will need to download and install the updates manually from the CCDC website: https://www.ccdc.cam.ac.uk/support-and-resources/downloads/
ConQuest: Advanced Searching of Structures in the Cambridge Structural Database
You have access to ConQuest, the primary program for searching and retrieving information from the CSD. Search options include:
Mercury: Crystal Structure Visualization, Exploration and Analysis Made Easy
You have access to Mercury, a visualization software that offers a comprehensive range of tools for 3D structure visualization, the exploration of crystal packing and the statistical analysis of CSD search data. Mercury allows to:
EnCIFer: Safely Check and Edit Crystallographic Information Files (CIFs)
You have access to EnCIFer that enables validation of CIFs and ensures that files are format-compliant for deposition with journals and databases or for storage in laboratory archives. EnCIFer allows to:
Mogul: Knowledge Base
You have access to Mogul that you can use to validate your experimental or predicted structures using experimentally-derived, peer-reviewed data. It can display distributions of important geometries based on the bond lengths, angles, ring geometries, and torsions of the expertly curated structures in the CSD.
IsoStar: Knowledge-based Library of Intermolecular Interactions
You have access to IsoStar, is a web application that allows displaying the probability of occurrence and spatial characteristics of interactions between pairs of chemical functional groups.These scatterplots facilitate the rapid exploration and assessment of intermolecular interactions without the need to construct complex search queries, or carry out detailed data analyses. IsoStar contains information on intermolecular interactions derived from both small-molecule crystal structures in the CSD and from protein-ligand interactions observed in the Protein Data Bank (PDB). Interaction energies, computed using intermolecular perturbation theory (IMPT), are also included for many important systems.
SuperStar: Knowledge-based Pharmacophore Generation and Prediction of Intermolecular Interactions
You have access to SuperStar that uses crystallographic information about non-bonded interactions to generate interaction maps within protein binding sites or around small molecules, i.e. it predicts ‘hot-spots’ where a chosen interaction type is particularly favorable.
CSD-CrossMiner: Versatile Pharmacophore Query Tool for Successful Drug Discovery
You have access to CSD-CrossMiner, a tool that allows crystal structure databases such as the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB) to be searched in terms of pharmacophore queries. Intuitive pharmacophore queries describing, among others, protein−ligand interaction patterns, ligand scaffolds, or protein environments can be built and modified interactively. Matching crystal structures are overlaid onto the pharmacophore query and visualized as soon as they are available, enabling the user to quickly modify a hypothesis on the fly. This delivers an overall interactive search experience with application in the areas of interaction searching, scaffold hopping or the identification of novel fragments for specific protein environments.
For example use cases, read: Korb O, Kuhn B, Hert J, Taylor N, Cole J, Groom C & Stahl M “Interactive and Versatile Navigation of Structural Databases” J Med Chem, 2016, 59(9):4257, DOI: 10.1021/acs.jmedchem.5b01756.
Hermes: 3D Visualization Package for Macromolecules
You have access to Hermes that allows displaying protein and other macromolecular structures in 3D from the most common file types including PDB files, Mol2 files, Mol files and contoured surface files (.acnt format). The flexible and comprehensive controls let you navigate around the structure and modify the appearance to display ribbons, wireframe or spacefill to suit your needs. Hermes also hosts interfaces to GOLD, Mogul, SuperStar, and descriptors for GOLD docking poses.
GOLD: Protein-Ligand Docking Software
You have access to GOLD that allows structure-based docking screens of large compound libraries.
CSD Python API
You have access to the CSD Python API (Application Programming Interface) that enables you to create, or download from the CSD Python API user forum CSD-driven analyses and workflows, tailor them to your needs and then publish them to your own menu in Mercury for specialist visualization and easier communication.