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 protein that helps cells break down damaged proteins, and when mutated it causes a rare inherited disease combining muscle weakness, bone problems, and dementia. This analysis examined the R155H variant using AI structure prediction, achieving good overall confidence (83% average), though this specific variant appears extremely rare with only one occurrence in nearly 1.5 million chromosomes analyzed. The mutation sits in a critical region of the protein that likely affects how VCP recognizes and processes damaged proteins, potentially explaining how it leads to toxic protein accumulation in muscles and brain cells.
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: 1461880
Disease Associations
677 totalShowing 5 of 677 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 R155H variant shows well-folded ATPase domains (pLDDT 83.0) with pathogenic mutation in D1 domain and expected C-terminal disorder.
Average pLDDT of 83.0 with 87% high-confidence residues indicates a well-folded core structure. The C-terminal region (residues 708-806) shows reduced confidence, consistent with predicted disorder.
Lower confidence in the C-terminal tail (residues 708-806) aligns with annotated disordered regions and contains the UBXN6 interaction site and PIM motif (residues 797-806). The structured N-terminal and central domains show high confidence, while the Gly-rich segment (residues 777-793) displays moderate flexibility.
The R155H mutation occurs in the well-folded N-terminal domain, likely affecting the D1 ATPase domain stability and nucleotide binding. This pathogenic variant is associated with inclusion body myopathy with Paget disease and frontotemporal dementia (IBMPFD).
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 are highly relevant as they provide mechanistic insights into VCP mutations causing IBMPFD/ALS/FTD through various pathways including protein quality control dysfunction, hypoxic stress, and structural destabilization. While none specifically study the R155H variant, they establish the broader pathogenic mechanisms and clinical spectrum of VCP mutations that would apply to understanding R155H pathogenesis.
Clinical Agent (1)
The first baseline data collection for VCP R155H represents the initial systematic documentation of clinical, biomarker, and functional parameters in patients carrying this pathogenic variant before significant disease progression occurs. This baseline establishment is clinically crucial because VCP R155H causes a multi-system degenerative disease (IBMPFD/ALS/FTD) with highly variable onset and progression rates, making it essential to capture pre-symptomatic or early-stage measurements to track disease evolution and identify potential therapeutic intervention windows. These baseline measurements will serve as the reference point for monitoring disease progression and evaluating treatment efficacy in future clinical trials targeting VCP-related neurodegeneration.
Structural Agent (1)
AlphaFold structure update: Baseline check: 1 structure(s) found
Supplements Agent (1)
The therapeutic landscape for VCP R155H in IBMPFD/ALS/FTD shows very limited supplement or peptide research. While multiple preprints examine VCP biology and inhibition mechanisms, only one study tangentially addresses herbal/nutritional interventions, and none specifically target the R155H variant with dietary supplements or therapeutic peptides.
Synthesis Agent (1)
Synthesis of 5 findings (clinical, literature, peptides, structural, supplements): Synthesis JSON could not be parsed; raw response is in agent logs....
Peptide Agent (1)
VCP R155H: 10 known binders (top: 24.0 nM); 1 candidate peptides designed