KpATCC43816 Protein target profile

3-deoxy-8-phosphooctulonate synthase

Accession: VK055_0220

Gene: AIK78848.1 kdsA 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GUB6
Length 284
Pocket druggability (P2Rank · AlphaFold DB model) 0.871
Metabolic reactions 1
Chokepoint Yes
Direct ligand evidence 0 59 total records
Functional annotation 1 EC 4 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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

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
4.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
95.423 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
96.63 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) 0.871
Structure A0A0H3GUB6
Pocket Pocket 1
Druggability (FPocket) 0.305
Structure A0A0H3GUB6
Pocket Pocket 2
ColabFold model
P2Rank 0.882 · Pocket 1
FPocket 0.244 · Pocket 3
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 219 / 4744 genomes with a hit
Prevalence 4.6%

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a producing chokepoint reaction in Biosynthesis of various nucleotide sugars, no isoenzyme backup detected, more central than 94.7% of genes in this genome, no human homolog detected.

Relative network centrality 94.7% more central than 94.7% of genes in this genome
Chokepoint Chokepoint gene
Catalyzed reaction

1 reaction 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.

MKQKVVSIGDINVANDLPFVLFGGMNVLESRDLAMRICEHYVTVTQKLGIPYVFKASFDKANRSSIHSYRGPGLEEGMKIFQELKQTFGVKIITDVHEASQAQPVADVVDVIQLPAFLARQTDLVEAMAKTGAVINVKKPQFVSPGQMGNIVDKFIEGGNDKVILCDRGANFGYDNLVVDMLGFGVMKKASNNSPVIFDVTHALQCRDPFGAASGGRRAQVSELARAGMAVGIAGLFIEAHPDPDHAKCDGPSALPLDKLEPFLKQMKAIDDLVKSFDELDTSK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
  • GO:0008676 Catalysis of the reaction: D-arabinose 5-phosphate + H2O + phosphoenolpyruvate = 8-phospho-3-deoxy-D-manno-oct-2-ulosonate + 2 H+ + phosphate.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0019294 The chemical reactions and pathways resulting in the formation of keto-3-deoxy-D-manno-octulosonic acid, an acidic sugar present in lipopolysaccharides of the outer membranes of some Gram-negative bacteria.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
1 283 FunFam G3DSA:3.20.20.70:FF:000058 2-dehydro-3-deoxyphosphooctonate aldolase
10 275 Pfam PF00793 DAHP synthetase I family
10 275 InterPro IPR006218 DAHP synthetase I/KDSA
18 275 NCBIfam TIGR01362 3-deoxy-8-phosphooctulonate synthase
18 275 InterPro IPR006269 3-deoxy-8-phosphooctulonate synthase
1 283 Gene3D G3DSA:3.20.20.70 Aldolase class I
1 283 InterPro IPR013785 Aldolase-type TIM barrel
13 277 Hamap MF_00056 2-dehydro-3-deoxyphosphooctonate aldolase [kdsA].
13 277 InterPro IPR006269 3-deoxy-8-phosphooctulonate synthase
6 282 PANTHER PTHR21057 PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
6 282 InterPro IPR006269 3-deoxy-8-phosphooctulonate synthase
3 277 SUPERFAMILY SSF51569 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.

Download VMD script Full viewer

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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
0.871
Likely same site as FPocket 2 2.1 Å 22 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.006
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #2
0.305 Unusual size
Likely same site as P2Rank 1 2.1 Å 22 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_A0A0H3GUB6
AlphaFold DB full sequence Viewing
ColabFold VK055_0220
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.

59 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 9 records from similar proteins
Structural ligands 9 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
1NT PDB via homolog 416.2 Da · LogP -4.19 · TPSA 272.0 Open detail RCSB PDB
2PG PDB via homolog Detail RCSB PDB
A5P PDB via homolog Detail RCSB PDB
AZI PDB via homolog Detail RCSB PDB
E4P PDB via homolog Detail RCSB PDB

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
1NT RCSB PDB O66496 416.2 Da LogP -4.19 TPSA 272.0 1 viol. ✓ Clean C([C@H]([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)O…
2PG RCSB PDB O66496 186.1 Da LogP -1.46 TPSA 124.3 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)OP(=O)(O)O)O
A5P RCSB PDB O66496 232.1 Da LogP -2.83 TPSA 147.7 1 viol. ✓ Clean C([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)O
AZI RCSB PDB Q9WYH8 42.0 Da LogP 0.87 TPSA 58.7 ✓ Ro5 Alert [N-]=[N+]=[N-]
E4P RCSB PDB Q9WYH8 200.1 Da LogP -1.98 TPSA 124.3 ✓ Ro5 ✓ Clean C([C@H]([C@H](C=O)O)O)OP(=O)(O)O
FPE RCSB PDB P0A715 188.0 Da LogP -0.48 TPSA 104.1 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)OP(=O)(O)O)F
KD0 RCSB PDB Q3JP68 318.2 Da LogP -3.42 TPSA 202.0 1 viol. ✓ Clean C([C@H]([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)O…
PAI RCSB PDB P0A715 415.2 Da LogP -4.71 TPSA 248.9 1 viol. ✓ Clean C([C@H]([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)O…
PEP RCSB PDB P0A715 168.0 Da LogP -0.31 TPSA 104.1 ✓ Ro5 ✓ Clean C=C(C(=O)O)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.

Cross-references

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