Protein target profile

VK055_2206

fructose-1,6-bisphosphate aldolase, class II

Genome: KpATCC43816 Gene: fba AIK80811.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 4 reactions UniProt A0A0H3GJ12
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Length 286
Pocket druggability 0.946
Metabolic reactions 4
Chokepoint No
Direct ligand evidence 0 10 total records
Functional annotation 0 EC 6 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

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

Main supporting evidence

Central metabolic position More central than 99.4% of genes in this genome. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Strong predicted binding pocket FPocket selected-pocket score 0.95. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Microbiome similarity 144 of 4744 screened genomes (3.0%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.95) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.16.

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
3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
51.761 Higher values support similarity to known essential genes.
DEG E-value
1.2e-101 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
94.79 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.946
Structure A0A0H3GJ12
Pocket Pocket 1
P2Rank 0.16
Structure A0A0H3GJ12
Pocket Pocket 1
ColabFold model
FPocket 0.578 · Pocket 14
P2Rank 0.092 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 144 / 4744 genomes with a hit
Prevalence 3.0%

Cross-references

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

Sequence

UniProt A0A0H3GJ12

Pathways

KEGG R02568 BioCyc RXN-8631 KEGG R01068 BioCyc F16ALDOLASE-RXN KEGG R01829 BioCyc SEDOBISALDOL-RXN BioCyc RXN-19916

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 99.4% of genes in this genome, no human homolog detected.

Relative network centrality 99.4% more central than 99.4% of genes in this genome
Chokepoint Not a chokepoint
Pathways
Carbon fixation by Calvin cycle Fructose and mannose metabolism Glycolysis / Gluconeogenesis Methane metabolism Pentose phosphate pathway
Catalyzed reactions

4 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MLVSMKDMLQHALRDGYAVGQFNINNLEWVGAVLSTAQQCRSPVILGVSGGTVKHMLGLKCIHDIVVNAMEYLHIDVPVALHLDHGTSREACEAAIAAGFSSIMFDGSHLPFRENLAITRHLVTLAHSKGISVEAELGTIAGSEDGIVNSEVIYADPQECYTLVTETKVDCLAAALGSTHGLYKGKARLGFTEMKAIAEQVKVPLVLHGGTGIADEDMRRAIACGTAKINVNTENMYAWCQQVKAIFAADTGHDVNDPRKVIAQGLQPVREMIARRMALFGSEQRY

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0030388 The chemical reactions and pathways involving fructose 1,6-bisphosphate, also known as FBP. The D enantiomer is a metabolic intermediate in glycolysis and gluconeogenesis.
  • GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
  • GO:0016832 Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.
  • GO:0008270 Binding to a zinc ion (Zn).
  • GO:0004332 Catalysis of the reaction: beta-D-fructose 1,6-bisphosphate = D-glyceraldehyde 3-phosphate + dihydroxyacetone phosphate.
  • GO:0006096 The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
5 283 CDD cd00947 TBP_aldolase_IIB
5 283 InterPro IPR000771 Fructose-bisphosphate aldolase, class-II
2 285 NCBIfam TIGR01859 class II fructose-1,6-bisphosphate aldolase
2 285 InterPro IPR011289 Fructose-1,6-bisphosphate aldolase, class 2
1 286 PIRSF PIRSF001359 F_bP_aldolase_II
1 286 InterPro IPR000771 Fructose-bisphosphate aldolase, class-II
1 285 NCBIfam TIGR00167 ketose-bisphosphate aldolase
1 285 InterPro IPR000771 Fructose-bisphosphate aldolase, class-II
3 284 Pfam PF01116 Fructose-bisphosphate aldolase class-II
3 284 InterPro IPR000771 Fructose-bisphosphate aldolase, class-II
1 285 Gene3D G3DSA:3.20.20.70 Aldolase class I
1 285 InterPro IPR013785 Aldolase-type TIM barrel
3 283 SUPERFAMILY SSF51569 Aldolase
1 282 PANTHER PTHR30304 D-TAGATOSE-1,6-BISPHOSPHATE ALDOLASE

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 · FPocket

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

Site 1 FPocket #1
0.946
Likely same site as P2Rank 1 6.1 Å 7 shared residues 64% of smaller site
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Surrounding area
Site 2 FPocket #5
0.389
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.16
Likely same site as FPocket 1 6.1 Å 7 shared residues 64% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.123
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Surrounding area
Site 3 P2Rank #3
0.068
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Surrounding area
Site 4 P2Rank #4
0.06
Likely same site as FPocket 1 6.3 Å 8 shared residues 89% of smaller site
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Surrounding area
Site 5 P2Rank #5
0.057
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Surrounding area
Residue sets
UniProt: Active site:82-82 Proton donor
UniProt: Binding site:104-104
UniProt: Binding site:134-134
UniProt: Binding site:178-178
UniProt: Binding site:179-179
UniProt: Binding site:206-206
UniProt: Binding site:207-209
UniProt: Binding site:228-231
UniProt: Binding site:83-83
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_A0A0H3GJ12
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_2206
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.

10 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 4 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 6 similarity-based ZINC candidates
Best available ligand signal
13P PDB via homolog 170.1 Da · LogP -1.34 · TPSA 104.1 Open detail RCSB PDB
FLC PDB via homolog Detail RCSB PDB
MLT PDB via homolog Detail RCSB PDB
PGH PDB via homolog Detail RCSB PDB
ZINC71773889 ZINC proposed compound · Tanimoto 0.667 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
13P RCSB PDB
3Q94
A0A6H3AA11 170.1 Da LogP -1.34 TPSA 104.1 ✓ Ro5 ✓ Clean C(C(=O)COP(=O)(O)O)O
FLC RCSB PDB
4TO8
W8TRN9 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
MLT RCSB PDB
7NCC
Q6TV43 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)C(=O)O
PGH RCSB PDB
1GVF
P0AB74 171.0 Da LogP -1.40 TPSA 116.1 ✓ Ro5 ✓ Clean C(C(=O)NO)OP(=O)(O)O

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.