- Predicted Function
- Non-enzyme (p=0.99) — a pseudokinase. Astra recognises a kinase-like fold but declines to call it an active enzyme, matching SCYL3's known catalytically-dead status.
- Kinase Pocket
- Degenerate — medium confidence. A pocket in the kinase N-lobe (residues 58–85), but a low ATP-binding signal (0.15) and only medium pocket confidence (0.68) — consistent with a non-functional active site.
- Architecture
- Soluble; an N-terminal (pseudo)kinase domain (2–245) followed by four HEAT repeats — a scaffolding / protein-interaction module, not a catalyst.
- Modifications
- N-myristoylation at Gly2 (membrane / partner targeting); scattered phosphosites.
- Clean Signal
- Predominantly ordered (only a short disordered C-terminus); no amyloid.
Model-reported confidence for the headline calls (amber = the load-bearing prediction the rest of the profile builds on). These are model-estimated probabilities that rank and gate each call — not calibrated rates of experimental success.
The Gap
Why This Target Is Still Dark
SCYL3 (PACE1) is a kinase that probably isn't one. It carries a canonical protein-kinase domain and four HEAT repeats, but lacks the catalytic HRD motif — so it is classed as a pseudokinase, thought to act as a scaffold rather than an enzyme. It has no experimental structure in the PDB, no known substrate, and is understudied (IDG Tbio). Yet it is disease-relevant: SCYL3 binds the C-terminus of ezrin (hence "PACE1") and localises to the lamellipodia of metastatic cancer cells with F-actin and CD44, and drives hepatocellular-carcinoma progression as a binding partner and regulator of ROCK2.
That combination — a kinase-shaped protein that may not be a kinase — is exactly where prediction earns its keep: everything below is computed from the canonical 742-residue sequence and derived structural predictions, with no experimental SCYL3 structure used as input. The first question — real enzyme or scaffold? — is one the sequence can answer.
Architecture & Topology
How the Sequence Is Organised
| Element | Residues | Note |
|---|---|---|
| Pseudokinase domain | 2–245 | N-terminal protein-kinase fold; degenerate ATP pocket in the N-lobe; lacks the catalytic HRD motif. |
| HEAT repeats | 250–410 | Four HEAT repeats — a scaffolding / protein-interaction module, not a catalyst. |
| C-terminal region | 411–742 | Scaffolding C-terminus; short disordered tail (728–742); no amyloid signal. |
The Predicted Pocket
The Predicted (Degenerate) Active Site
A degenerate ATP site: the pocket sits in the N-lobe where ATP would normally bind, but at only medium confidence (0.68) and with a low ATP-binding signal (0.15). Astra classifies SCYL3 as a non-enzyme (p=0.99) — a scaffold. For a pseudokinase that discrimination is the whole question, and it reframes any drug-discovery approach: target the fold for interaction disruption or allosteric control, not for ATP-competitive inhibition.
Site: Kinase N-lobe where ATP would normally bind (residues 58–85); ATP-binding signal only 0.15
Post-Translational & Structural Features
Specific, Testable Residues
- N-myristoylation at Gly2. An N-terminal lipid anchor that targets the pseudokinase to membranes and partner complexes — consistent with its reported lamellipodial localisation.
- Dispersed phosphosites across the HEAT-repeat and C-terminal regions — a likely regulatory layer over the scaffolding function.
- Predominantly ordered; short disordered C-terminus (728–742). No amyloid signal — the folded core is a viable target for structural work.
Recommended Experimental Follow-Up
An Orphan Sequence, Turned Into a Ranked Plan
Each prediction is paired with the experiment that would test it and the readout to watch for.
| Prediction | Experiment | Readout |
|---|---|---|
| Non-enzyme / pseudokinase call | In-vitro kinase assay (± ATP, generic substrate) | Confirm absence of catalytic activity |
| Degenerate ATP pocket (58–85) | ATP-analogue binding / thermal-shift | Weak or no nucleotide binding |
| HEAT-repeat scaffold | Interaction proteomics (ezrin, ROCK2, actin/CD44) | Map the protein-interaction network |
| N-myristoylation at Gly2 | G2A mutant | Mislocalisation — loss of membrane / lamellipodial targeting |
Scope & Limitations
What This Is — and Isn't
- Prediction, not experiment. These are computational hypotheses to prioritise experiments — not a substitute for a structure or an assay. No result here has been validated in the wet lab.
- The pseudokinase call is a prediction. Astra flags SCYL3 as a non-enzyme, consistent with its missing HRD motif — but a direct kinase assay is needed to confirm it is catalytically dead. A residual or conditional activity cannot be excluded from sequence alone.
- Biology caveats. The disease role rests on cancer cell-line studies; SCYL3's partners and the consequences of disrupting them are only partly mapped. Treat the therapeutic case as a hypothesis.
All predictions were generated with Orbion's Astra suite from the canonical SCYL3 sequence (UniProt Q8IZE3), using AlphaFold-derived structural features. Reported values are model outputs; model internals are out of scope.
References
- [1]UniProt Consortium. UniProtKB entry Q8IZE3 (SCYL3, human). uniprot.org.
- [2]Pharos (Illuminating the Druggable Genome). SCYL3 target record — Tbio. pharos.nih.gov.
- [3]SCYL3, as a novel binding partner and regulator of ROCK2, promotes hepatocellular carcinoma progression. JHEP Reports 4(12) (2022). https://pmc.ncbi.nlm.nih.gov/articles/PMC9691429/