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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 2020.0 release contains over 1,034,174 entries (1,016,168 unique structures), an increase of more than 60,000 entries! The new release contains the following new features:

1) The launch of polyhedral display in Mercury

2) Python 3 compatibility

3) Support in the CSD Python API for all types of 3D query available in ConQuest

4) Extension of th CSD-CrossMiner database

5) Seamless, flexible searching of CSD and PDB data

6) Molecular interaction maps in the CSD Python API

6) Polymer expansion in Mercury

Read more and see CSD in numbers.

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)

Read more about WebCSD.

                                                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 2020 Release for your operating system. 
     

Note: The 2020.0 CSD release will require a complete re-installation of the software and data. You will need the Customer No. and Activation Key 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 2020.0 CSD Release installer contains:

  • The Cambridge Structural Database, Version 5.41
  • ConQuest 2.0.4
  • Mercury 4.3.0
  • enCIFer 1.7.4
  • IsoStar 2.3.4 
  • Mogul 1.8.4
  • Conformer Generator 1.3.4
  • Hermes 1.10.4
  • GOLD 5.8.0
  • CSD Ligand Overlay 1.2.4
  • SuperStar 2.2.4 
  • DASH 3.4.4 (Windows only)
  • CSD Python API 3.0.0
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 file and instructions for Linux. (See instructions 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 Crossminer

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 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 and refer to installation notes. For Option 2, refer to the table below:

Windows MacOSX Linux

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

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

Download 64-bit installation files for Linux. 

 

CSD Python API

This release enables:

• Python 3.7 as the default version for all CSD applications

• The CSD Python API will be Python 3 enabled straightaway at the point of installation 

• Easy integration with other key scientific Python packages

This release will incorporate Python 3 by default, with the miniconda version of the CSD Python API bundled within the 2020.0 CSD Release running on Python 3.7. This means that the CSD Python API will be Python 3 enabled straight away at the point of installation and easy to integrate with other key scientific Python packages like TensorFlow, scikit-learn, matplotlib, pandas and RDKit.

Find out more here: https://www.ccdc.cam.ac.uk/Community/blog/python-3-and-the-csd

For CSD Python API example scripts, download .zip file.


To download Python 3.7. CSD Python API 3.0.0, use Option 1 or Option 2 and refer to installation notes. For Option 2, refer to the table below:

Windows MacOS 64-bit Linux

Download pip installer and conda installer

Download pip installer and conda installer

Download pip installer and conda installer