# CVE-2026-3408: Open Babel NULL pointer dereference in CDXML OBAtom::GetExplicitValence

Source: https://junglewise.ai/threats/cve-2026-3408-open-babel-null-pointer-dereference-in-cdxml-obatom  
Publisher: Junglewise Threat Intelligence, https://junglewise.ai/threats  
Published: 2026-06-30. Updated: 2026-06-30  
License: CC BY 4.0 with a link back

CVE-2026-3408 · Severity: medium · CVSS 5.5 · Published 2026-06-30

Open Babel, a widely used library for processing chemical data files, contains a flaw in how it handles certain file formats. An attacker could create a specially crafted chemical data file (CDXML) that, when opened by a user or processed by a service, causes the application to crash. This could lead to a denial of service, impacting the availability of research tools or automated chemistry services.

Technologies: [openbabel (PyPI)](https://junglewise.ai/threats/technologies/openbabel). Vendors: [PyPI](https://junglewise.ai/threats/vendors/pypi).

## Quick answers

**Is CVE-2026-3408 exploited in the wild?** No. Junglewise Threat Intelligence has no report of CVE-2026-3408 being exploited in the wild.

**How severe is CVE-2026-3408?** Medium severity, with a CVSS score of 5.5, published 30 June 2026.

**Which products and versions are affected?** openbabel (PyPI) < 3.2.0, ECOSYSTEM:introduced=0,fixed=3.2.0.

**Is there a fix for CVE-2026-3408?** Yes. openbabel (PyPI): upgrade to 3.2.0 or later. Junglewise finds every place you run it, drafts the upgrade and applies it once you approve.

**How is CVE-2026-3408 attacked?** It is attacked with local access, in a software library.

**Am I affected by CVE-2026-3408?** Check whether you run openbabel (PyPI) at an affected version. Junglewise does that check for you around the clock: connect your code, cloud and domains, and it matches new vulnerabilities like this one against what you actually run and tells you when one reaches you.

## How to fix

- openbabel (PyPI): upgrade to 3.2.0 or later

  ```sh
  pip install "openbabel>=3.2.0"
  ```


## Technical details

A NULL pointer dereference exists in Open Babel's CDXML file format parser within the `OBAtom::GetExplicitValence` method. The vulnerability is triggered when the parser encounters a malformed fragment in a CDXML file, causing it to invoke the method on a NULL atom pointer. Exploitation requires a victim to open a malicious CDXML file using the `obabel` CLI tool, the `OBConversion` API, or any of its language bindings (e.g., Python, Java, C#). The issue is fixed in version 3.2.0.

## Affected products

- Open Babel openbabel <= 3.1.1

## Identifiers

- CVE-2026-3408
- GHSA-rxpr-wq63-jr7p
- PYSEC-2026-2791

## Timeline

- 2026-05-26: patched: Version 3.2.0 released
- 2026-05-27: advisory: Initial GitHub Advisory published
- 2026-06-30: disclosed: Full advisory details published/updated

## References

- [https://api.github.com/users/VedantMadane](https://api.github.com/users/VedantMadane)
- [https://github.com/VedantMadane](https://github.com/VedantMadane)
- [https://api.github.com/users/VedantMadane/gists%7B/gist_id%7D](https://api.github.com/users/VedantMadane/gists%7B/gist_id%7D)
- [https://api.github.com/users/VedantMadane/repos](https://api.github.com/users/VedantMadane/repos)
- [https://avatars.githubusercontent.com/u/6527493?v=4](https://avatars.githubusercontent.com/u/6527493?v=4)
- [https://api.github.com/users/VedantMadane/events%7B/privacy%7D](https://api.github.com/users/VedantMadane/events%7B/privacy%7D)

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- [Open Babel out-of-bounds write in MOPAC output parser](https://junglewise.ai/threats/cve-2022-46293-open-babel-out-of-bounds-write-in-mopac-output-parser)
- [Open Babel out-of-bounds write in Gaussian translationVectors](https://junglewise.ai/threats/cve-2022-46291-open-babel-out-of-bounds-write-in-gaussian-translationvectors)