AI-ACCELERATED DRUG DISCOVERY
Available from Reaxense
This protein is integrated into the Receptor.AI ecosystem as a prospective target with high therapeutic potential. We performed a comprehensive characterization of LIM domain-binding protein 3 including:
1. LLM-powered literature research
Our custom-tailored LLM extracted and formalized all relevant information about the protein from a large set of structured and unstructured data sources and stored it in the form of a Knowledge Graph. This comprehensive analysis allowed us to gain insight into LIM domain-binding protein 3 therapeutic significance, existing small molecule ligands, relevant off-targets, and protein-protein interactions.
Fig. 1. Preliminary target research workflow
2. AI-Driven Conformational Ensemble Generation
Starting from the initial protein structure, we employed advanced AI algorithms to predict alternative functional states of LIM domain-binding protein 3, including large-scale conformational changes along "soft" collective coordinates. Through molecular simulations with AI-enhanced sampling and trajectory clustering, we explored the broad conformational space of the protein and identified its representative structures. Utilizing diffusion-based AI models and active learning AutoML, we generated a statistically robust ensemble of equilibrium protein conformations that capture the receptor's full dynamic behavior, providing a robust foundation for accurate structure-based drug design.
Fig. 2. AI-powered molecular dynamics simulations workflow
3. Binding pockets identification and characterization
We employed the AI-based pocket prediction module to discover orthosteric, allosteric, hidden, and cryptic binding pockets on the protein’s surface. Our technique integrates the LLM-driven literature search and structure-aware ensemble-based pocket detection algorithm that utilizes previously established protein dynamics. Tentative pockets are then subject to AI scoring and ranking with simultaneous detection of false positives. In the final step, the AI model assesses the druggability of each pocket enabling a comprehensive selection of the most promising pockets for further targeting.
Fig. 3. AI-based binding pocket detection workflow
4. AI-Powered Virtual Screening
Our ecosystem is equipped to perform AI-driven virtual screening on LIM domain-binding protein 3. With access to a vast chemical space and cutting-edge AI docking algorithms, we can rapidly and reliably predict the most promising, novel, diverse, potent, and safe small molecule ligands of LIM domain-binding protein 3. This approach allows us to achieve an excellent hit rate and to identify compounds ready for advanced lead discovery and optimization.
Fig. 4. The screening workflow of Receptor.AI
Receptor.AI, in partnership with Reaxense, developed a next-generation technology for on-demand focused library design to enable extensive target exploration.
The focused library for LIM domain-binding protein 3 includes a list of the most effective modulators, each annotated with 38 ADME-Tox and 32 physicochemical and drug-likeness parameters. Furthermore, each compound is shown with its optimal docking poses, affinity scores, and activity scores, offering a detailed summary.
LIM domain-binding protein 3
partner:
Reaxense
upacc:
O75112
UPID:
LDB3_HUMAN
Alternative names:
Protein cypher; Z-band alternatively spliced PDZ-motif protein
Alternative UPACC:
O75112; A2TDB7; A6NIV4; B4E3K3; Q5K6N9; Q5K6P0; Q5K6P1; Q96FH2; Q9Y4Z3; Q9Y4Z4; Q9Y4Z5
Background:
LIM domain-binding protein 3, also known as Protein cypher or Z-band alternatively spliced PDZ-motif protein, plays a crucial role in striated muscle. It functions as an adapter, linking protein kinase C-mediated signaling to the cytoskeleton through its LIM domains. This protein's involvement in muscle structure and function underscores its importance in maintaining muscular integrity.
Therapeutic significance:
LIM domain-binding protein 3 is implicated in several muscular and cardiovascular diseases, including Cardiomyopathy, dilated, 1C, with or without left ventricular non-compaction, Left ventricular non-compaction 3, and Myopathy, myofibrillar, 4. These associations highlight the protein's potential as a target for therapeutic intervention in treating muscle-related disorders and cardiomyopathies.
