KKB

The Kinase Knowledgebase (KKB) is Eidogen-Sertanty's database of kinase structure-activity relationship (SAR) and chemical synthesis data, compiled from scientific literature and patents. It represents a gene-family wide implementation of Eidogen-Sertanty's proprietary web-based technology for the capture, curation, and display of biological activity and chemical synthesis data. The KKB is designed to support medicinal chemists and computational scientists across all stages of drug discovery projects.

The Q4 2025 release of the Kinase Knowledgebase contains data drawn from 10,270 journal articles and patents, covering 576 unique kinase targets with assay data and over 791,000 unique kinase molecules sourced from patents and articles. The database holds nearly 2.95 million biological activity data points and over 100,000 annotated assay protocols.

Database Content (Q4 2025 Release)

• Journal articles and patents: 10,270
• Biological activity data points: 2,949,253
• Unique kinase molecules with annotated assay data: 447,140
• Unique kinase molecules from patents and articles (with or without bioactivity data): 791,020
• Unique kinase targets with assay data: 576
• Annotated assay protocols: 100,714

Chemical Structure Search Capabilities

• Substructure search within the KKB
• Exact structure search
• Similar structure search
• AI keyword search
• SMILES string retrieval
• Structure drawing powered by Ketcher, an open-source molecule editor

Data Quality and Curation

All SAR data in the KKB undergoes rigorous quality control. Each data point is associated with detailed bioassay protocols and is classified according to the following attributes:

• Standardized gene name
• Binding mode
• Assay type
• Additional in vitro data, including cellular potency and cell line information
• Efficacy data from appropriate animal models

In vitro enzyme activity data — particularly IC50 values — are selected for the development of QSAR models (ePotency and eSelectivity). Cell-based activity and toxicity data are used for the development of advanced activity models (eADME and eTox). The curation process also captures chemical synthesis steps for kinase inhibitors with detailed experimental procedures, organized by protocols of generic reaction sequences incorporating synthetically feasible reagents. This approach generates all specific examples from a patent as well as a broader ensemble of structures representing the patent space, with synthetic pathways structurally linked to biological information.

Human Kinome Tree Views

• Visualization of kinases with biological activity data in the KKB
• Distribution of KKB bioactivity data points by kinase family

Applications in Drug Discovery

• Map out the patent landscape around inhibitors for kinase targets of interest
• Organize known inhibitors into scaffold groups, including detailed synthesis steps
• Use predicted properties and eScreen® data to prioritize compounds for synthesis or purchase
• Utilize large quantities of descriptive SAR data to enable scaffold jumping

Value Across Project Stages

• At the lead discovery stage, the KKB provides an overview of published knowledge and patents around kinase targets of therapeutic importance, supporting understanding of the knowledge space around a target and its relevant anti-targets
• Inhibitor structural data supports grouping of known inhibitors into scaffold groups and planning around patentable chemotypes
• During lead optimization, the KKB helps prioritize compounds for synthesis or purchase based on predicted properties
• Nearly 50 kinase-specific eScreen® modules have been developed from the KKB content, supporting potency and selectivity prediction, lead optimization, and scaffold jumping

The KKB is designed for use by all scientists in a drug discovery team, including those without specialist computational training. It is available in multiple data formats for direct access and integration into in-house databases. Licensing terms and product demonstrations are available on request from Eidogen-Sertanty.