KpATCC43816 Protein target profile

putative carboxysome structural protein with predicted role in ethanolamine utilization

Accession: VK055_4729

Gene: AIK83263.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GRF9
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Length 206
Pocket druggability (P2Rank · AlphaFold DB model) 0.715
Direct ligand evidence 0 3 total records
Functional annotation 0 EC 2 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Second pocket predictor agrees P2Rank predicted binding-site probability 0.71. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 1 structural and 0 bioactivity records.

Risks to review

Microbiome similarity 159 of 4744 screened genomes (3.4%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.71) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant. Best pocket may be a modeling artifact FPocket selected-pocket score 0.43, but this pocket's geometry is unusually large/diffuse compared to this protein's other predicted pockets — may reflect a low-confidence or disordered model region rather than a real cavity.

Evidence coverage

Core evidence streams are available for this target.
Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
No hit
Gut microbiome similarity
3.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
92.718 Higher values support similarity to known essential genes.
DEG E-value
1.35e-140 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
98.0 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.715
Structure A0A0H3GRF9
Pocket Pocket 1
Druggability (FPocket) 0.432
Structure A0A0H3GRF9
Pocket Pocket 1
ColabFold model
P2Rank 0.767 · Pocket 1
FPocket 0.279 · Pocket 10
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 159 / 4744 genomes with a hit
Prevalence 3.4%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MRVIASVNDGFARELKLPSHIRSLGLITADSDDVTYIAADEATKQAMVEVVYGRSLYAGAAHGPSPTAGEVLIMLGGPNPAEVRAGLDAMMAHIEGGAAFQWANDAQDTAFLAHVVSRTGSYLSSAAGIALGDPIAYLVAPPLEATFGIDAAMKSADVQLVTYVPPPSETNYSAAFLTGSQAACKAACNAFTDAVLDIARHPVQRA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Subcellular localization

Localization
Unknown

Gene Ontology (GO)

2
  • GO:0031469 An organelle found in bacteria consisting of a proteinaceous coat containing metabolic enzymes whose purpose is the sequestration or concentration of metabolites and which has the appearance of a polygonal granule by electron microscopy.
  • GO:0005198 The action of a molecule that contributes to the structural integrity of a complex.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

23 records
Show feature table
Start End DB Term Name
95 206 Gene3D G3DSA:3.30.70.1710 -
95 206 InterPro IPR037233 CcmK-like superfamily
1 204 NCBIfam TIGR04502 ethanolamine utilization microcompartment protein EutL
1 204 InterPro IPR030983 Bacterial microcompartment shell protein EutL
118 204 CDD cd07050 BMC_EutL_repeat2
1 100 ProSiteProfiles PS51931 Bacterial microcompartment (BMC) circularly permuted domain profile.
1 100 InterPro IPR044870 Bacterial microcompartment (BMC) circularly permuted domain
22 119 SMART SM00877 BMC_2
22 119 InterPro IPR000249 Bacterial microcompartment domain
129 206 SMART SM00877 BMC_2
129 206 InterPro IPR000249 Bacterial microcompartment domain
146 198 SUPERFAMILY SSF143414 CcmK-like
146 198 InterPro IPR037233 CcmK-like superfamily
1 206 PIRSF PIRSF012290 EutL_PduB
1 206 InterPro IPR009193 Bacterial microcompartment shell protein, EutL/PduB type
101 202 ProSiteProfiles PS51931 Bacterial microcompartment (BMC) circularly permuted domain profile.
101 202 InterPro IPR044870 Bacterial microcompartment (BMC) circularly permuted domain
1 94 Gene3D G3DSA:3.30.70.1710 -
1 94 InterPro IPR037233 CcmK-like superfamily
23 94 Pfam PF00936 BMC domain
23 94 InterPro IPR000249 Bacterial microcompartment domain
149 195 Pfam PF00936 BMC domain
149 195 InterPro IPR000249 Bacterial microcompartment domain

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.715
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Surrounding area
Pocket 2 P2Rank #2
0.559
Likely same site as FPocket 1 1.4 Å 16 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.078
Show in viewer
Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #1
0.432 Unusual size
Likely same site as P2Rank 2 1.4 Å 16 shared residues 100% of smaller site
Show in viewer
Surrounding area
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GRF9
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4729
ColabFold — — full sequence — Loaded

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

3 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 1 records from similar proteins
Structural ligands 1 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 2 similarity-based ZINC candidates
Best available ligand signal
ETA PDB via homolog 61.1 Da · LogP -1.06 · TPSA 46.2 Open detail RCSB PDB
ZINC2385445 ZINC proposed compound · Tanimoto 0.500 Detail ZINC
ZINC34196183 ZINC proposed compound · Tanimoto 0.500 Detail ZINC

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
ETA RCSB PDB
4TME
Q8XLZ0 61.1 Da LogP -1.06 TPSA 46.2 ✓ Ro5 ✓ Clean C(CO)N

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GRF9