Skip to main content
Library Research Guides

Cambridge Structural Database

A powerful and flexible resource to discover the knowledge contained within more than 500,000 crystal structures.

Library Contact

Yulia Sevryugina's picture
Yulia Sevryugina
Contact:
3162 Shapiro Library,
919 S. University Ave., Ann Arbor, MI, 48109-1185
7346155694
Website

Access to Cambridge Structural Database

Cambridge Structural Database (CSD) is a world wide repository of small molecule crystal structures hosted by Cambridge Crystallographic Data Center (CCDC). The 2018 release contains over 900,000 entries (CSD version 5.39) – an increase of more than 60,000 entries! Read What's new in 2018 release. University of Michigan has unlimited site license to access CSD. You may access the database via either of the following two means.

1. WebCSD - the online portal to the CSD (Click here to access WebCSD)

(NOTE: as of April 2017, the only Web browsers that are fully compatible with WebCSD are Internet Explorer v.6.0 or later and Safari v.4.0 or later, due to WebCSD's reliance on Java applets for structure searching.  If you prefer not to use either of these browsers, we recommend that you install CSDS on your local computer as described below. CCDC reports that they will remove the reliance on Java in WebCSD 2.0; no release date is yet available.)

                                                OR
2. Install Cambridge Structural Database System (CSDS) on your own computer.

Two Options to Download

  • Option 1: Request links to download the software at: http://www.ccdc.cam.ac.uk/support-and-resources/csdsdownloads/. You will need our site number and confirmation code, and your uniquename@umich.edu 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.) 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.
  • Option 2: Follow links in the Table below to the Box folder containing the software. Click on "Continue" under "Log in: Part of University of Michigan", login with your unique name and UMICH password, and download the Cambridge Structural Database System 2018 Release for your operating system. 
     

Note: You will need the Site No. and Confirmation Code to register for the system after it is installed. Start Mercury or ConQuest or Mogul to register.  Please read the release_install.pdf document after you download the software for troubleshooting problems during installation. 

The availability of the CSDS for different operating systems is explained in the box below.

The difference between WebCSD and the CSDS client access is explained in the tab WebCSD and CSDS.

Availability of CSDS for different operating systems

The 2018 CSD Release installer contains:

  • The Cambridge Structural Database, Version 5.39
  • ConQuest 1.20
  • Mercury 3.10
  • enCIFer 1.6.1
  • IsoStar 2.2.5 (Server is Linux 32-bit only)
  • Mogul 1.7.3
  • Conformer Generator 1.2
  • Hermes 1.9
  • GOLD 5.6
  • SuperStar 2.1.6 (Windows and Linux only)
  • DASH 3.3.7 (Windows only)
  • CSD Python API 1.5 (not supported on Windows XP)
Windows MacOSX Linux

Download .zip file and instructions for Windows 7/8 and 10, Windows Vista, or Windows XP .

Download .dmg file and instructions for Mac OS X 10.8, 10.9, 10.10, and 10.11.

Download 32-bit and 64-bit installation files and instructions for Linux. (See the release_install.pdf for Linux system supported.)

Note:

For downloading from M+Box Folder 

  • Use IE 9 or later, the current version of Firefox or Google Chrome. Older browsers may NOT work.
  • These large files (over 6 Gb) may take between 15 min and several hours to download, depending on the speed of your Internet connection.
  • Following the links in the table above, click on "Continue" button under "Login: Part of University of Michigan" and log in with your unique name and password.

Updating to Mac OS X 10.10 can cause an existing XQuartz installation to become corrupted. For OS X 10.8 and later a suitable X11 server can be downloaded from http://xquartz.macosforge.org.

Find more troubleshooting tips on the CCDC Support page.

CSD updates for the 2018 CSD Release

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: http://www.ccdc.cam.ac.uk

You can find out more about the updates from this blog article on the CCDC website: https://www.ccdc.cam.ac.uk/Community/blog/2018-02-frequent-releases/

CSD Crossminer

This year you have access to CSD-Crossminer. CSD-CrossMiner is a novel 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 visualised 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, please see:
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.

To download CSD Crossminer (64-bit only), use Option 1 or Option 2. For Option 2, refer to the table below:

Windows MacOSX Linux

Download .zip file and instructions for Windows 7/8 and 10, Windows Vista, or Windows XP .

Download .dmg file and instructions for Mac OS X 10.8, 10.9, 10.10, and 10.11.

Download 64-bit installation files and instructions for Linux. 

 

Additional Resources

Users interested in setting up their own local IsoStar server on Linux can access the installer either using Option 1 or Option 2.

 

Advanced Python users can also download pip and conda packages to install into their own Python. More details on these packages can be found on our CSD Python API forum here: CSD Python API Forum

 

Relibase for easy searching of protein-ligand complexes.can be accessed via http://relibase.ccdc.cam.ac.uk

 

PreQuest is only available upon request. If you need access to it, please get in contact with the CCDC support team at support@ccdc.cam.ac.uk