KpATCC43816 Protein target profile

benzoate 1,2-dioxygenase electron transfer component

Accession: VK055_0613

Gene: benC AIK79236.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 3 reactions UniProt A0A0H3GQC4
Length 338
Pocket druggability (P2Rank · AlphaFold DB model) 0.742
Metabolic reactions 3
Chokepoint Yes
Direct ligand evidence 0 57 total records
Functional annotation 0 EC 3 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.

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
Hit
Human identity (%)
24.498 Lower values reduce human off-target concern.
Human E-value
1.17e-07
Gut microbiome similarity
0.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
38.757 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
92.34 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) 0.742
Structure A0A0H3GQC4
Pocket Pocket 1
Druggability (FPocket) 0.852
Structure A0A0H3GQC4
Pocket Pocket 19
ColabFold model
P2Rank 0.665 · Pocket 1
FPocket 0.728 · Pocket 11
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 20 / 4744 genomes with a hit
Prevalence 0.4%

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 Benzoate degradation, no isoenzyme backup detected.

Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Chokepoint gene
Catalyzed reactions

3 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.

MTFNIALNFEDGVTRFIQCNAGEKVLDAAYRQKVNLPMDCSDGVCGTCKCHCASGEYDLGEDYLDEALSDDEAQNRQVLTCQMVPTSDCVIDVPVAAAQCKTTLANIGAQVRQVNLLSDTAIELVVALDEPLAFLPGQYVNIQVPGTPHVRAYSFSSQPGSLEGRFLIRNVPGGMMSQWLTQRARPGDRLTLSGPMGSFYLRHGERPLLMLAGGTGLAPLLSMLHTLQTQGSQRPVMLLYGVTRDCDLVKTDALDTFTQQLTGYRWLPVVADENSTCPQRGFVTDHLDDAMLNNGDVDIYLCGPPPMVSAVATALRDRGITPAGFWYEKFIASQSAAA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

3
  • GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

43 records
Show feature table
Start End DB Term Name
40 48 ProSitePatterns PS00197 2Fe-2S ferredoxin-type iron-sulfur binding region signature.
40 48 InterPro IPR006058 2Fe-2S ferredoxin, iron-sulphur binding site
110 200 Pfam PF00970 Oxidoreductase FAD-binding domain
110 200 InterPro IPR008333 Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain
104 202 ProSiteProfiles PS51384 Ferredoxin reductase-type FAD binding domain profile.
104 202 InterPro IPR017927 FAD-binding domain, ferredoxin reductase-type
109 331 CDD cd06209 BenDO_FAD_NAD
109 331 InterPro IPR047683 Benzoate 1,2-dioxygenase reductase, FAD/NAD binding domain
194 203 PRINTS PR00410 Phenol hydroxylase reductase family signature
234 243 PRINTS PR00410 Phenol hydroxylase reductase family signature
298 306 PRINTS PR00410 Phenol hydroxylase reductase family signature
134 146 PRINTS PR00410 Phenol hydroxylase reductase family signature
209 228 PRINTS PR00410 Phenol hydroxylase reductase family signature
151 158 PRINTS PR00410 Phenol hydroxylase reductase family signature
16 92 PANTHER PTHR47354 NADH OXIDOREDUCTASE HCR
101 197 Gene3D G3DSA:2.40.30.10 Translation factors
3 97 ProSiteProfiles PS51085 2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
3 97 InterPro IPR001041 2Fe-2S ferredoxin-type iron-sulfur binding domain
210 312 Pfam PF00175 Oxidoreductase NAD-binding domain
210 312 InterPro IPR001433 Oxidoreductase FAD/NAD(P)-binding
78 203 SUPERFAMILY SSF63380 Riboflavin synthase domain-like
78 203 InterPro IPR017938 Riboflavin synthase-like beta-barrel
200 332 SUPERFAMILY SSF52343 Ferredoxin reductase-like, C-terminal NADP-linked domain
200 332 InterPro IPR039261 Ferredoxin-NADP reductase (FNR), nucleotide-binding domain
5 94 SUPERFAMILY SSF54292 2Fe-2S ferredoxin-like
5 94 InterPro IPR036010 2Fe-2S ferredoxin-like superfamily
3 333 NCBIfam NF040810 benzoate 1,2-dioxygenase electron transfer component BenC
17 92 CDD cd00207 fer2
17 92 InterPro IPR001041 2Fe-2S ferredoxin-type iron-sulfur binding domain
198 330 Gene3D G3DSA:3.40.50.80 -
198 330 InterPro IPR039261 Ferredoxin-NADP reductase (FNR), nucleotide-binding domain
1 100 Gene3D G3DSA:3.10.20.30 -
1 100 InterPro IPR012675 Beta-grasp domain superfamily
209 228 PRINTS PR00371 Flavoprotein pyridine nucleotide cytochrome reductase signature
209 228 InterPro IPR001709 Flavoprotein pyridine nucleotide cytochrome reductase
298 306 PRINTS PR00371 Flavoprotein pyridine nucleotide cytochrome reductase signature
298 306 InterPro IPR001709 Flavoprotein pyridine nucleotide cytochrome reductase
151 158 PRINTS PR00371 Flavoprotein pyridine nucleotide cytochrome reductase signature
151 158 InterPro IPR001709 Flavoprotein pyridine nucleotide cytochrome reductase
134 144 PRINTS PR00371 Flavoprotein pyridine nucleotide cytochrome reductase signature
134 144 InterPro IPR001709 Flavoprotein pyridine nucleotide cytochrome reductase
10 86 Pfam PF00111 2Fe-2S iron-sulfur cluster binding domain
10 86 InterPro IPR001041 2Fe-2S ferredoxin-type iron-sulfur binding 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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
0.742
Likely same site as FPocket 19 5.2 Å 28 shared residues 97% of smaller site
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.662
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.304
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.254
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.177
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #19
0.852 Unusual size
Likely same site as P2Rank 1 5.2 Å 28 shared residues 97% 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_A0A0H3GQC4
AlphaFold DB full sequence Viewing
ColabFold VK055_0613
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.

57 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
BTB PDB via homolog 209.2 Da · LogP -3.01 · TPSA 104.4 Open detail RCSB PDB
DGG PDB via homolog Detail RCSB PDB
ECN PDB via homolog Detail RCSB PDB
FDA PDB via homolog Detail RCSB PDB
FES 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
BTB RCSB PDB Q03304 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
DGG RCSB PDB P39662 735.0 Da LogP 9.75 TPSA 148.8 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@…
ECN RCSB PDB P39662 381.7 Da LogP 5.80 TPSA 27.1 1 viol. ✓ Clean c1cc(ccc1COC(Cn2ccnc2)c3ccc(cc3Cl)Cl)Cl
FDA RCSB PDB P22868 787.6 Da LogP -1.75 TPSA 363.3 3 viol. ✓ Clean Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C…
FES RCSB PDB A0A076MZ01 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
KKK RCSB PDB P39662 531.4 Da LogP 4.21 TPSA 69.1 1 viol. Alert CC(=O)N1CCN(CC1)c2ccc(cc2)OC[C@H]3CO[C@](O3)(Cn…
X89 RCSB PDB P39662 416.1 Da LogP 6.45 TPSA 27.1 1 viol. ✓ Clean c1cc(c(cc1Cl)Cl)CO[C@@H](Cn2ccnc2)c3ccc(cc3Cl)Cl

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.