KpATCC43816 Protein target profile

bacterial regulatory, luxR family protein

Accession: VK055_0030

Gene: AIK78661.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GS53
Length 240
Pocket druggability (P2Rank · AlphaFold DB model) 0.826
Direct ligand evidence 0 94 total records
Functional annotation 0 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
1.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
94.52 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) 0.826
Structure A0A0H3GS53
Pocket Pocket 1
Druggability (FPocket) 0.8
Structure A0A0H3GS53
Pocket Pocket 1
ColabFold model
P2Rank 0.82 · Pocket 1
FPocket 0.811 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 63 / 4744 genomes with a hit
Prevalence 1.3%

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.

MRDNDFFSWRRDMLHQFQSMATGEEVYNLLQRETEALEYDYYTLCVRHPVPFTRPRVTFQSTYPRAWMSHYQAENYFAIDPVLRPENFMRGHLPWNDSLFRDAPALWDGARDHGLQKGVTQCLTLPNHAQGFLSVSANNRLPGGYPEDELELRLRTLTELSLLTLLRLEDEMVMPPEMKFSRRELEILKWTAEGKTSAEVAMILSISENTVNFHQKNMQRKFNAPNKTQIACYAVATGLI

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

4
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0051301 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
  • GO:0045893 Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
24 157 Pfam PF03472 Autoinducer binding domain
24 157 InterPro IPR005143 Transcription factor LuxR-like, autoinducer-binding domain
1 176 Gene3D G3DSA:3.30.450.80 -
1 176 InterPro IPR036693 Transcription factor LuxR-like, autoinducer-binding domain superfamily
177 240 FunFam G3DSA:1.10.10.10:FF:000297 DNA-binding transcriptional activator SdiA
180 235 CDD cd06170 LuxR_C_like
180 235 InterPro IPR000792 Transcription regulator LuxR, C-terminal
180 234 Pfam PF00196 Bacterial regulatory proteins, luxR family
180 234 InterPro IPR000792 Transcription regulator LuxR, C-terminal
98 239 PANTHER PTHR44688 -
177 240 Gene3D G3DSA:1.10.10.10 -
177 240 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
194 210 PRINTS PR00038 LuxR bacterial regulatory protein HTH signature
194 210 InterPro IPR000792 Transcription regulator LuxR, C-terminal
180 194 PRINTS PR00038 LuxR bacterial regulatory protein HTH signature
180 194 InterPro IPR000792 Transcription regulator LuxR, C-terminal
210 222 PRINTS PR00038 LuxR bacterial regulatory protein HTH signature
210 222 InterPro IPR000792 Transcription regulator LuxR, C-terminal
8 170 SUPERFAMILY SSF75516 Pheromone-binding domain of LuxR-like quorum-sensing transcription factors
8 170 InterPro IPR036693 Transcription factor LuxR-like, autoinducer-binding domain superfamily
177 234 SMART SM00421 luxrmega5
177 234 InterPro IPR000792 Transcription regulator LuxR, C-terminal
164 240 SUPERFAMILY SSF46894 C-terminal effector domain of the bipartite response regulators
164 240 InterPro IPR016032 Signal transduction response regulator, C-terminal effector
194 221 ProSitePatterns PS00622 LuxR-type HTH domain signature.
194 221 InterPro IPR000792 Transcription regulator LuxR, C-terminal
173 238 ProSiteProfiles PS50043 LuxR-type HTH domain profile.
173 238 InterPro IPR000792 Transcription regulator LuxR, C-terminal

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
0.826
Likely same site as FPocket 1 1.2 Å 15 shared residues 100% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.031
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.007
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
0.8
Likely same site as P2Rank 1 1.2 Å 15 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_A0A0H3GS53
AlphaFold DB full sequence Viewing
ColabFold VK055_0030
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.

94 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 44 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 39 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
480 PDB via homolog 218.3 Da · LogP 1.24 · TPSA 66.8 Open detail RCSB PDB
482 PDB via homolog Detail RCSB PDB
EVY PDB via homolog Detail RCSB PDB
HTF PDB via homolog Detail RCSB PDB
LAE 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
480 RCSB PDB Q8XBD0 218.3 Da LogP 1.24 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC(=O)OC[C@H](CO)O
482 RCSB PDB Q8XBD0 213.2 Da LogP 0.18 TPSA 72.5 ✓ Ro5 ✓ Clean CCCC(=O)CC(=O)N[C@H]1CCOC1=O
EVY RCSB PDB Q9RMS5 339.5 Da LogP 4.76 TPSA 55.4 ✓ Ro5 ✓ Clean CCCCCCCC[C@H](CCCCCC)C(=O)N[C@H]1CCOC1=O
HTF RCSB PDB P07026 227.3 Da LogP 1.78 TPSA 55.4 ✓ Ro5 ✓ Clean CCCCCCCC(=O)N[C@H]1CCOC1=O
LAE RCSB PDB Q8XBD0 241.3 Da LogP 0.96 TPSA 72.5 ✓ Ro5 ✓ Clean CCCCCC(=O)CC(=O)N[C@H]1CCOC1=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.