KpATCC43816 Protein target profile

3-deoxy-7-phosphoheptulonate synthase

Accession: VK055_4577

Gene: AIK83115.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GWX1
Length 356
Pocket druggability (P2Rank · AlphaFold DB model) 0.583
Metabolic reactions 1
Chokepoint Yes
Direct ligand evidence 0 58 total records
Functional annotation 1 EC 7 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
5.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
52.326 Higher values support similarity to known essential genes.
DEG E-value
3.28e-136 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
96.79 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) 0.583
Structure A0A0H3GWX1
Pocket Pocket 1
Druggability (FPocket) 0.669
Structure A0A0H3GWX1
Pocket Pocket 1
ColabFold model
P2Rank 0.5 · Pocket 1
FPocket 0.624 · Pocket 3
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 243 / 4744 genomes with a hit
Prevalence 5.1%

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 Phenylalanine, tyrosine and tryptophan biosynthesis, more central than 95.6% of genes in this genome, no human homolog detected.

Relative network centrality 95.6% more central than 95.6% 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.

MQKDALNNVHITDEHVLMTPEQLKAEFPLSVEQEAQIAHARQTISDIIAGRDPRLLVVCGPCSIHDPEAAIEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEGGLKIARRLLVELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVGFKNGTDGSLATAINAMRAAAMPHRFVGINQAGQVCLLQTQGNPNGHVILRGGKAPNYGPEDVAKCEKEMAQAGLKPSLMVDCSHGNSNKDFRRQPAVAESVVAQIKDGNRSIIGLMIESNIHEGNQSSEQPREAMKYGVSVTDACISWETTEALLRELDKDLRGHLAARLV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0009073 The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
  • GO:0003849 Catalysis of the reaction: D-erythrose 4-phosphate + H2O + phosphoenolpyruvate = 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate + phosphate.
  • 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0042802 Binding to an identical protein or proteins.
  • GO:0008652 The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
  • GO:0009423 The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
9 349 NCBIfam TIGR00034 3-deoxy-7-phosphoheptulonate synthase
9 349 InterPro IPR006219 DAHP synthase, class 1
8 345 SUPERFAMILY SSF51569 Aldolase
1 353 Gene3D G3DSA:3.20.20.70 Aldolase class I
1 353 InterPro IPR013785 Aldolase-type TIM barrel
1 354 FunFam G3DSA:3.20.20.70:FF:000005 Phospho-2-dehydro-3-deoxyheptonate aldolase
2 349 PANTHER PTHR21225 PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE DAHP SYNTHETASE
2 349 InterPro IPR006219 DAHP synthase, class 1
38 340 Pfam PF00793 DAHP synthetase I family
38 340 InterPro IPR006218 DAHP synthetase I/KDSA
1 354 PIRSF PIRSF001361 DAHP_synthase
1 354 InterPro IPR006219 DAHP synthase, class 1

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
0.583
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Surrounding area
Pocket 2 P2Rank #2
0.183
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Surrounding area
Pocket 3 P2Rank #3
0.16
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Surrounding area
Pocket 4 P2Rank #4
0.039
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Surrounding area
Pocket 5 P2Rank #5
0.028
Likely same site as FPocket 1 1.0 Å 11 shared residues 100% of smaller site
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.669
Likely same site as P2Rank 5 1.0 Å 11 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_A0A0H3GWX1
AlphaFold DB full sequence Viewing
ColabFold VK055_4577
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.

58 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 8 records from similar proteins
Structural ligands 8 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
0V5 PDB via homolog 170.1 Da · LogP -0.43 · TPSA 104.1 Open detail RCSB PDB
DTY PDB via homolog Detail RCSB PDB
G3P PDB via homolog Detail RCSB PDB
GZ3 PDB via homolog Detail RCSB PDB
PEP 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
0V5 RCSB PDB Q9K169 170.1 Da LogP -0.43 TPSA 104.1 ✓ Ro5 ✓ Clean C[C@H](C(=O)O)OP(=O)(O)O
DTY RCSB PDB P32449 181.2 Da LogP 0.35 TPSA 83.5 ✓ Ro5 ✓ Clean c1cc(ccc1C[C@H](C(=O)O)N)O
G3P RCSB PDB P32449 172.1 Da LogP -1.55 TPSA 107.2 ✓ Ro5 ✓ Clean C([C@H](COP(=O)(O)O)O)O
GZ3 RCSB PDB Q9K169 166.1 Da LogP 0.15 TPSA 94.8 ✓ Ro5 ✓ Clean C/C(=C\P(=O)(O)O)/C(=O)O
PEP RCSB PDB Q9K169 168.0 Da LogP -0.31 TPSA 104.1 ✓ Ro5 ✓ Clean C=C(C(=O)O)OP(=O)(O)O
PEQ RCSB PDB Q9K169 170.1 Da LogP -0.43 TPSA 104.1 ✓ Ro5 ✓ Clean C[C@@H](C(=O)O)OP(=O)(O)O
PGA RCSB PDB P0AB91 156.0 Da LogP -0.82 TPSA 104.1 ✓ Ro5 ✓ Clean C(C(=O)O)OP(=O)(O)O
TMO RCSB PDB Q9K169 75.1 Da LogP 0.19 TPSA 23.1 ✓ Ro5 ✓ Clean C[N+](C)(C)[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.