01/3D Structure
? About the 3D Viewer
Mol* (pronounced "molstar") is an open-source molecular visualization tool used by the Protein Data Bank and AlphaFold Database. Learn more at molstar.org.
Controls:
- Rotate: Click and drag
- Zoom: Scroll wheel or pinch
- Pan: Right-click and drag (or two-finger drag)
- Reset: Double-click to reset view
What am I looking at?
This is a predicted 3D structure of the protein. The ribbon diagram shows the protein backbone—helices appear as coils, sheets as arrows, and loops as simple lines. The shape determines how the protein functions: where it binds to other molecules, how it catalyzes reactions, and how mutations might disrupt its activity.
Color legend:
The structure is colored by pLDDT confidence score, which indicates how confident AlphaFold is in each region's predicted position:
- Blue (>90): Very high confidence
- Cyan (70-90): Confident
- Yellow (50-70): Low confidence
- Orange (<50): Very low confidence, likely disordered
02/AI Analysis
TLDR
LRRK2 is a large enzyme that regulates cellular processes, and mutations in LRRK2 are the most common genetic cause of Parkinson's disease. We analyzed the G2019S variant (a change from glycine to serine at position 2019) in the kinase domain, which showed excellent structural prediction quality with an average confidence score of 90.6. This variant is relatively common in the population (found in approximately 1 in 2,400 chromosomes) and is known to increase the enzyme's activity, contributing to neuronal dysfunction in Parkinson's disease.
Detailed Analysis
03/Research Data
ClinVar Classification
Not found in ClinVar
Population Frequency
No population data available
Disease Associations
No disease associations found
AI Research Brief
04/AlphaFold Metrics
No visualization images available.
05/Domain Annotations
Structural Domains & Regions
Functional Sites
Binding Partners
Gene Ontology
06/Structural Caption
LRRK2 kinase G2019S variant shows high-confidence structure across all domains (pLDDT 90.6), with pathogenic mutation positioned in the kinase activation loop.
Average pLDDT of 90.6 with 95% (248/260) high-confidence residues indicates excellent overall model quality. The structure shows robust confidence across all major domains with minimal destabilization.
High confidence spans all functional regions including the 13 leucine-rich repeats (residues 983-1291), Roc GTPase domain (1328-1511), COR domain (1546-1740), protein kinase domain (1879-2138), and 7 WD40 repeats (2139-2497), suggesting well-ordered multi-domain architecture.
The G2019S mutation in the kinase domain activation loop is the most common Parkinson's disease-causing variant in LRRK2, increasing kinase activity approximately 2-3 fold while maintaining structural integrity of the catalytic domain.
07/Peptide Therapeutics
Aggregation Analysis
Aggregation propensity analysis identifies 1 hotspots (average score: 0.09) using Pawar+KyteDoolittle+charge algorithm.
08/Known Inhibitors
Known Binders from ChEMBL
09/Candidate Peptides
De Novo Peptide Design Pipeline
Pipeline: BoltzGen (de novo binder design) → Boltz-2 rescore → 8-gate wetlab filter → PK + BBB advisory gates. Target site selected from UniProt curated annotations, P2Rank pocket prediction, and aggregation propensity (in that priority order). Advisory gates annotate each candidate with estimated serum half-life, renal/immunogenicity risk, and (for CNS targets) a recommended blood-brain-barrier shuttle conjugation — without silently dropping designs.
Loading candidate statistics...
Sequences are withheld pending IP review. Full candidate data (sequences,
scores, CIF files) is available to authorized reviewers via the
/api/private/candidates/{fold_id} endpoint with
X-Private-Key.
Legacy candidates (charge-complementary)
Target Region
Residues 64–68 (0.78 aggregation score)Candidate ID
CP-03B-001
(7 residues · computational design)
10/Agent Findings
Literature Agent (1)
These papers are highly relevant to understanding LRRK2 G2019S pathogenic mechanisms and clinical implications in PD. They reveal critical ethnic variations in G2019S prevalence, elucidate molecular pathways linking LRRK2 kinase activity to GCase regulation and Rab8a phosphorylation, identify CSF LRRK2 as a progression biomarker, and demonstrate that LRRK2 variants do not significantly alter DBS treatment responses. Collectively, they advance precision medicine approaches for LRRK2-associated PD through mechanistic insights and clinical biomarker development.
Clinical Agent (1)
No summary available
Structural Agent (1)
AlphaFold structure update: Baseline check: 1 structure(s) found
Supplements Agent (1)
The therapeutic landscape for LRRK2 G2019S in Parkinson's disease is dominated by small molecule kinase inhibitors rather than dietary supplements or peptides. NEU-411 represents the primary active pharmacological approach in Phase 2 testing for this specific mutation. Emerging preclinical research suggests potential for lipid-based nutritional interventions targeting the N-acylphosphatidylethanolamine pathway, though no clinical trials of supplements or peptides specifically for LRRK2 G2019S are currently active.
Synthesis Agent (1)
Synthesis of 5 findings (clinical, literature, peptides, structural, supplements): The LRRK2 G2019S variant represents one of the most clinically actionable targets in Parkinson's dis...
Peptide Agent (1)
03B LRRK2 KINASE: 10 known binders (top: 0.4 nM); 1 candidate peptides designed