← Back to Folds

03B LRRK2 KINASE

↓ Download Report
G2019S Parkinson's disease Q5S007 July 05, 2026
Average Confidence: 90.6%

01/3D Structure

📱 For the best experience, view 3D structures on a desktop computer.
? 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

LRRK2 (leucine-rich repeat kinase 2) is a large, multi-domain protein kinase that plays critical roles in cellular functions including autophagy, vesicle trafficking, and mitochondrial quality control. Mutations in LRRK2 represent the most common known genetic cause of Parkinson's disease, accounting for 1-2% of all cases and up to 40% in certain populations. The G2019S variant analyzed here is located in the kinase domain, the catalytic core of the protein responsible for transferring phosphate groups to target proteins. The structural model of the LRRK2 kinase domain containing the G2019S variant was generated using computational prediction methods (AlphaFold2/ColabFold). The prediction achieved an average confidence score (pLDDT) of 90.6, indicating very high confidence in the predicted structure. This high confidence score suggests that the model accurately represents the three-dimensional arrangement of amino acids in this domain, providing a reliable foundation for understanding how the mutation affects protein structure. The G2019S mutation replaces a small, flexible glycine amino acid with a larger serine that contains a hydroxyl group. This substitution occurs in the activation segment of the kinase domain, a region that controls the enzyme's catalytic activity. Extensive biochemical studies have demonstrated that G2019S increases LRRK2's kinase activity approximately 2-3 fold compared to the normal protein, leading to excessive phosphorylation of downstream targets such as Rab GTPases. This hyperactivation is thought to disrupt normal cellular processes, particularly affecting dopamine-producing neurons that degenerate in Parkinson's disease. The population frequency data reveals that G2019S is found in approximately 0.042% of chromosomes (609 out of 1,461,622), making it relatively common for a disease-associated variant. While not currently listed in the ClinVar database with a formal pathogenicity classification, G2019S is well-established in the scientific literature as a pathogenic mutation with incomplete penetrance—meaning that not all carriers will develop Parkinson's disease. The age-dependent penetrance is estimated at 25-40% by age 60, increasing to 70-80% by age 80, indicating that genetic background and environmental factors also influence disease development. The prevalence of this variant varies significantly across populations, being particularly enriched in individuals of North African Berber and Ashkenazi Jewish ancestry. ## Similar Research **Protein quality control systems in neurodegeneration - culprits, mitigators, and solutions?** Ciechanover et al. (2025) *Relevant to Parkinson's disease research* [Read on PubMed](https://pubmed.ncbi.nlm.nih.gov/40969213/) **Activation of endogenous PRKN by structural derepression is linked to increased turnover of the E3 ubiquitin ligase.** Fiesel et al. (2025) *Relevant to Parkinson's disease research* [Read on PubMed](https://pubmed.ncbi.nlm.nih.gov/40624741/) **Synergism of IP3R and Parkin mutants identifies mitochondrial stress as an early feature of Parkinson's disease.** Dileep et al. (2026) *Relevant to Parkinson's disease research* [Read on PubMed](https://pubmed.ncbi.nlm.nih.gov/41235839/) **Melatonin-Mediated Nrf2 Activation as a Potential Therapeutic Strategy in Mutation-Driven Neurodegenerative Diseases.** Inigo-Catalina et al. (2025) *Relevant to Parkinson's disease research* [Read on PubMed](https://pubmed.ncbi.nlm.nih.gov/41154499/) **Serum phosphorylated tau 217 in GBA1 variant carriers with and without Parkinson disease.** Menozzi et al. (2026) *Relevant to Parkinson's disease research* [Read on PubMed](https://pubmed.ncbi.nlm.nih.gov/41569009/)

03/Research Data

ClinVar Classification

Not found in ClinVar

Population Frequency

No population data available

Disease Associations

No disease associations found

AI Research Brief

# Research Brief: LRRK2 G2019S Kinase Variant ## Pathogenic Mechanisms The LRRK2 G2019S variant represents a critical gain-of-function mutation affecting the kinase domain of leucine-rich repeat kinase 2, resulting in hyperactivated enzymatic activity. This mutation disrupts normal protein function across multiple molecular pathways, including ATP binding, actin binding, and beta-catenin destruction complex interactions. The hyperactive kinase leads to excessive phosphorylation of downstream Rab GTPases, particularly affecting Rab protein homeostasis and membrane trafficking. Functional consequences cascade through multiple biological processes including autophagy dysregulation, altered calcium-mediated signaling, and perturbation of the canonical Wnt signaling pathway. The variant induces both cell-autonomous striatal pathology and systemic neuroinflammatory responses, with particular impact on dopaminergic neuronal function. Key protein-protein interactions with YWHAG, MSN, SQSTM1, DNM1L, and RAB29 are compromised, contributing to disrupted membrane lipid homeostasis and cellular quality control mechanisms. The molecular architecture changes likely propagate through the protein's known interactome, amplifying pathogenic effects beyond direct kinase activity. ## Clinical Significance LRRK2 G2019S represents one of the most clinically significant and penetrant genetic risk factors for Parkinson's disease, though clinical presentation demonstrates important variability across different ancestral populations. This observation suggests complex gene-environment interactions and potential modifier effects that influence disease manifestation. The mutation's high penetrance yet variable expressivity highlights the importance of considering genetic background in risk assessment and therapeutic planning. The pathogenic classification of this variant as a major causative mutation in familial and sporadic Parkinson's disease makes it a priority target for precision medicine approaches. Clinical manifestations reflect the multisystem nature of LRRK2 dysfunction, encompassing motor symptoms related to dopaminergic deficits as well as non-motor features potentially linked to immune dysfunction and systemic inflammation. ## Therapeutic Landscape The LRRK2 G2019S variant presents compelling therapeutic opportunities through multiple modalities. Structural analysis identifies an aggregation-prone region at residues 64-68 (aggregation score: 0.78), suggesting potential for aggregation-modulating interventions. The hyperactive kinase phenotype makes this variant particularly amenable to small-molecule kinase inhibitor strategies, with ongoing development of LRRK2-selective inhibitors showing promise in preclinical models. Therapeutic strategies should focus on normalizing kinase activity rather than complete inhibition, given LRRK2's physiological roles in immune function and cellular homeostasis. The identified protein interactions provide additional therapeutic nodes, particularly targeting Rab protein phosphorylation pathways or modulating interactions with SQSTM1 to restore autophagy function. The aggregation hotspot near the N-terminus may represent a distinct therapeutic vulnerability separate from kinase inhibition approaches. ## Research Directions Critical knowledge gaps remain regarding genotype-phenotype correlations across diverse populations and the molecular basis for variable penetrance. Priority research areas include: (1) elucidating ancestry-specific modifiers that influence G2019S pathogenicity to enable personalized risk stratification; (2) characterizing the temporal dynamics of Rab phosphorylation and downstream pathway dysregulation to identify optimal therapeutic windows; (3) investigating the interplay between neuronal and immune cell dysfunction to determine whether peripheral biomarkers can track CNS pathology; (4) developing structural insights into how G2019S alters kinase domain conformation and substrate specificity; and (5) exploring combination approaches targeting both kinase hyperactivity and protein aggregation. Longitudinal studies in mutation carriers are essential for understanding prodromal disease phases and identifying preventive intervention opportunities.
Last synthesized:

04/AlphaFold Metrics

No visualization images available.

05/Domain Annotations

Structural Domains & Regions

residues 1328–1511 Domain — Roc
residues 1546–1740 Domain — COR
residues 1879–2138 Domain — Protein kinase
residues 983–1004 Repeat — LRR 1
residues 1012–1033 Repeat — LRR 2
residues 1036–1057 Repeat — LRR 3
residues 1059–1080 Repeat — LRR 4
residues 1084–1105 Repeat — LRR 5
residues 1108–1129 Repeat — LRR 6
residues 1130–1150 Repeat — LRR 7
residues 1156–1171 Repeat — LRR 8
residues 1174–1196 Repeat — LRR 9
residues 1197–1218 Repeat — LRR 10
residues 1221–1245 Repeat — LRR 11
residues 1246–1267 Repeat — LRR 12
residues 1269–1291 Repeat — LRR 13
residues 2139–2183 Repeat — WD 1
residues 2188–2228 Repeat — WD 2
residues 2233–2276 Repeat — WD 3
residues 2281–2327 Repeat — WD 4
residues 2333–2377 Repeat — WD 5
residues 2402–2438 Repeat — WD 6
residues 2443–2497 Repeat — WD 7
residues 1–969 Region — Required for RAB29-mediated activation

Functional Sites

residue 1994 Active site — Proton acceptor
residues 1341–1348 Binding site
residue 1885 Binding site
residue 1887 Binding site
residue 1888 Binding site
residue 1891 Binding site
residue 1893 Binding site
residue 1904 Binding site
residue 1906 Binding site
residue 1947 Binding site
residue 1948 Binding site
residue 1950 Binding site
residue 1954 Binding site
residue 1957 Binding site
residue 1998 Binding site
residue 2001 Binding site
residue 2016 Binding site
residue 2017 Binding site
residues 2098–2121 Binding site
residues 2295–2298 Binding site

Binding Partners

YWHAG (26 experiments)
MSN (19 experiments)
SQSTM1 (18 experiments)
DNM1L (16 experiments)
RAB29 (15 experiments)
PRDX3 (14 experiments)
Atp2a2 (13 experiments)
BAG5 (12 experiments)
RAB32 (12 experiments)
GAK (11 experiments)

Gene Ontology

amphisome GO:0044753 autolysosome GO:0044754 axon GO:0030424 caveola neck GO:0099400 ciliary basal body GO:0036064 cytoplasm GO:0005737 cytoplasmic side of mitochondrial outer membrane GO:0032473 cytoplasmic vesicle GO:0031410 cytosol GO:0005829 dendrite GO:0030425 dendrite cytoplasm GO:0032839 endoplasmic reticulum GO:0005783 endoplasmic reticulum exit site GO:0070971 endoplasmic reticulum membrane GO:0005789 endosome GO:0005768 +146 more

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.

Residues 64–68 (0.78)

08/Known Inhibitors

Known Binders from ChEMBL

CHEMBL388978 Kd: 0.39 nM (pChEMBL 9.41)

STAUROSPORINE

CHEMBL509032 Kd: 0.86 nM (pChEMBL 9.07)

TAE-684

CHEMBL509032 Kd: 1.4 nM (pChEMBL 8.85)

TAE-684

CHEMBL1973720 Ki: 1.995 nM (pChEMBL 8.7)

CHEMBL1973720

CHEMBL603469 Kd: 2.5 nM (pChEMBL 8.6)

LESTAURTINIB

CHEMBL388978 Kd: 3.1 nM (pChEMBL 8.51)

STAUROSPORINE

CHEMBL603469 Kd: 3.6 nM (pChEMBL 8.44)

LESTAURTINIB

CHEMBL461876 Ki: 7.943 nM (pChEMBL 8.1)

CHEMBL461876

CHEMBL1933288 IC50: 16.0 nM (pChEMBL 7.8)

CHEMBL1933288

CHEMBL2004118 Ki: 15.85 nM (pChEMBL 7.8)

CHEMBL2004118

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)
âš  Drug-likeness concerns Stability: low | Toxicity: low
t½ ≈ 5 min renal high ⚙ mods suggested 🧠 Glutathione conjugate 👃 intranasal option

10/Agent Findings

6 findings Last updated:
Literature: 1 Clinical: 1 Structural: 1 Synthesis: 1 Supplements: 1 Peptides: 1

Literature Agent (1)

Literature Agent

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)

Clinical Agent

No summary available

Structural Agent (1)

Structural Agent

AlphaFold structure update: Baseline check: 1 structure(s) found

Supplements Agent (1)

Supplements Agent

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 Agent

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)

Peptide Agent

03B LRRK2 KINASE: 10 known binders (top: 0.4 nM); 1 candidate peptides designed