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
VCP is a cellular protein that helps break down and recycle damaged proteins, and mutations in VCP cause a devastating group of inherited diseases affecting muscle, bone, and brain function (collectively called IBMPFD), as well as related conditions like ALS and frontotemporal dementia. This analysis examined the R191Q variant using AlphaFold2 structure prediction (average confidence 82.9%), finding a moderately confident structural model. This specific variant was recently identified in a patient with semantic dementia, a rare language-focused form of dementia, and is extremely rare in the general population (seen in only 1 out of 1.5 million chromosomes), suggesting it may be disease-causing though it has not yet been officially classified by expert clinical databases.
Detailed Analysis
Works Cited
Similar Research
03/Research Data
ClinVar Classification
Not found in ClinVar
Population Frequency
6.84e-07
Extremely rare (<0.01%)
AC: 1 / AN: 1461866
Disease Associations
2081 totalShowing 5 of 2081 associations
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
VCP R191Q variant shows well-folded N-terminal and AAA+ domains with predicted C-terminal disorder encompassing UBXN6 binding and PIM motif regions.
Average pLDDT of 82.9 with 85% high-confidence residues indicates a well-predicted core structure. The C-terminal region (residues 708-806) shows reduced confidence, consistent with predicted disorder.
Known disordered regions (708-727, 768-806) align with lower confidence predictions. The UBXN6 interaction site and PIM motif (797-806) fall within the disordered C-terminus, suggesting these regions adopt structure upon binding.
The R191Q substitution replaces a charged arginine with polar glutamine in the N-terminal domain, potentially affecting local electrostatics and protein-protein interactions while preserving overall fold stability.
07/Peptide Therapeutics
Aggregation Analysis
Aggregation propensity analysis identifies 1 hotspots (average score: 0.02) 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 265–269 (0.80 aggregation score)Candidate ID
CP-VCP-001
(7 residues · computational design)
10/Agent Findings
Literature Agent (1)
These papers directly characterize the VCP R191Q variant's role in IBMPFD/ALS/FTD, documenting its specific clinical presentation (semantic dementia), early pathogenic mechanisms (hypoxic stress in astrocytes, protein quality control dysfunction), and population genetics. They demonstrate that R191Q expands the phenotypic spectrum of VCP-related disease and reveal novel therapeutic targets including HIF-1α signaling and VCP-mediated protein clearance pathways.
Clinical Agent (1)
The establishment of first baseline data collection for VCP R191Q is clinically significant because it enables longitudinal tracking of disease progression patterns in patients carrying this pathogenic variant associated with inclusion body myopathy with Paget's disease and frontotemporal dementia (IBMPFD), ALS, and FTD. This baseline data will allow clinicians to identify early biomarkers, establish natural history parameters, and measure therapeutic responses in future interventional trials, which is critical given the variable age of onset and phenotypic heterogeneity seen with VCP mutations. Having systematic baseline measurements will improve patient counseling regarding prognosis and help optimize timing for supportive interventions across the multisystem manifestations of this disease.
Structural Agent (1)
AlphaFold structure update: Baseline check: 1 structure(s) found
Supplements Agent (1)
The therapeutic landscape for VCP R191Q in IBMPFD/ALS/FTD contexts shows limited direct supplement or peptide clinical trial activity. Current research focuses on understanding VCP inhibition mechanisms and identifying novel molecular targets like ZDHHC17-mediated S-acylation that could inform future peptide or small molecule therapeutic development. No active clinical trials testing dietary supplements, nutritional interventions, or peptide therapeutics specifically for VCP R191Q were identified in this dataset.
Synthesis Agent (1)
Synthesis of 1 findings (peptides): Synthesis JSON could not be parsed; raw response is in agent logs....
Peptide Agent (1)
VCP R191Q: 10 known binders (top: 24.0 nM); 1 candidate peptides designed