KpATCC43816 Protein target profile

bacterial regulatory, luxR family protein

Accession: VK055_2292

Gene: AIK80896.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GNS7
Length 881
Pocket druggability (P2Rank · AlphaFold DB model) 0.921
Direct ligand evidence 0 60 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
No hit
Gut microbiome similarity
0.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
86.84 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) 0.921
Structure A0A0H3GNS7
Pocket Pocket 1
Druggability (FPocket) 0.899
Structure A0A0H3GNS7
Pocket Pocket 7
ColabFold model
P2Rank 0.928 · Pocket 1
FPocket 0.794 · Pocket 41
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 4 / 4744 genomes with a hit
Prevalence 0.1%

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.

MLERPRLLQLLSPVQQCRLGVVCAGAGFGKTTLLAQWHQQMVAQGERIAWLSLDEDDDDVWQFIPYLLQALRPLYADWDADFWRDMEEQKLSSSEQLLAGLINQLHYCPHDVYLIIDDFHVINDRGVYEALGYLIKHAPAALHLIIGSRFHPNLALSQLQAQDQLVEIYDRDLQFTLEETKHYFSRTVALPLSNHHAQRLQSVTEGWIAGMKIASLSAELQNDPEHLLRNMHGGTRSIARYLKEVVLDPLPEEVLDFLVKTSFLSRLNAELCNAVTGRDDSKAMLAWIERHNLFLSALDEQGYWFRYHPLLQENLRTMLQQNNDIDRKQLHELASHWFVEQKLWSEAVRHALSAGKPVHSPVQDGASAQSLAEEGDIDTLISWMHHLPPSTDPSRIDLQINLAWALAHYFHFDESRQLLDNLDQMVLHHRDDLTRSTWCKLRVVRAICEAFAENIPESLAIVQPLLAEVPCGDTWVDGLICNILSYCHVVNQRYHDALEVQQHMPSPESPLDNLFVSVYRAFIIAQCHLCQGDLGKAGWYAEKTLRQAECYTGTQSTSGATLAPLLAEIAYECQRGDSPEHLLADRLEFIDRFSPPDALSRCYTYLARQALDNDMPYEAERLLEHAQRLAVSRGWQRLQAMLLAEQVRVRLQSGNFTGAEQLQRQLEQMAASFRMDAEHPCQRAIVMSASLSRSRLLLARGQAPQACVLLAEMVSDHESRGDGLTAARLRTLWSLALWNSGKSAAARTTFQPVVQLAEQQHLTGLFLDAGDTLQPLLIGMNESSSACKEKGGVHEPWADKRAPADGTPFNSGSPDIPGELSEREFQILQLIAEGQMNKEIARSLAISAETVKWHIKNIYAKLKVNSRTQAMSRALEMKLLD

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

3
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0005515 Binding to a protein.
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

29 records
Show feature table
Start End DB Term Name
834 850 InterPro IPR000792 Transcription regulator LuxR, C-terminal
850 862 PRINTS PR00038 LuxR bacterial regulatory protein HTH signature
850 862 InterPro IPR000792 Transcription regulator LuxR, C-terminal
820 834 PRINTS PR00038 LuxR bacterial regulatory protein HTH signature
820 834 InterPro IPR000792 Transcription regulator LuxR, C-terminal
834 850 PRINTS PR00038 LuxR bacterial regulatory protein HTH signature
3 159 Gene3D G3DSA:3.40.50.300 -
3 159 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
815 880 SUPERFAMILY SSF46894 C-terminal effector domain of the bipartite response regulators
815 880 InterPro IPR016032 Signal transduction response regulator, C-terminal effector
5 186 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
5 186 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
817 874 SMART SM00421 luxrmega5
817 874 InterPro IPR000792 Transcription regulator LuxR, C-terminal
814 881 Gene3D G3DSA:1.10.10.10 -
814 881 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
834 861 ProSitePatterns PS00622 LuxR-type HTH domain signature.
834 861 InterPro IPR000792 Transcription regulator LuxR, C-terminal
820 872 Pfam PF00196 Bacterial regulatory proteins, luxR family
820 872 InterPro IPR000792 Transcription regulator LuxR, C-terminal
428 790 Gene3D G3DSA:1.25.40.10 Tetratricopeptide repeat domain
428 790 InterPro IPR011990 Tetratricopeptide-like helical domain superfamily
443 778 Pfam PF17874 MalT-like TPR region
443 778 InterPro IPR041617 MalT-like TPR region
540 879 PANTHER PTHR44688 -
813 878 ProSiteProfiles PS50043 LuxR-type HTH domain profile.
813 878 InterPro IPR000792 Transcription regulator LuxR, C-terminal
820 876 CDD cd06170 LuxR_C_like
820 876 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.

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
0.921
Likely same site as FPocket 7 5.6 Å 30 shared residues 97% of smaller site
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.516
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.35
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.17
Likely same site as FPocket 32 1.0 Å 12 shared residues 86% of smaller site
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.146
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #7
0.899 Unusual size
Likely same site as P2Rank 1 5.6 Å 30 shared residues 97% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #32
0.407
Likely same site as P2Rank 4 1.0 Å 12 shared residues 86% 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_A0A0H3GNS7
AlphaFold DB full sequence Viewing
ColabFold VK055_2292
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.

60 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 10 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 5 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
BEZ PDB via homolog 122.1 Da · LogP 1.38 · TPSA 37.3 Open detail RCSB PDB
HL0 PDB via homolog Detail RCSB PDB
HL6 PDB via homolog Detail RCSB PDB
HLC PDB via homolog Detail RCSB PDB
HTF 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
BEZ RCSB PDB P06993 122.1 Da LogP 1.38 TPSA 37.3 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)O
HL0 RCSB PDB D3W065 255.4 Da LogP 2.56 TPSA 55.4 ✓ Ro5 ✓ Clean CCCCCCCCCC(=O)N[C@H]1CCOC1=O
HL6 RCSB PDB D3W065 199.2 Da LogP 1.00 TPSA 55.4 ✓ Ro5 ✓ Clean CCCCCC(=O)N[C@H]1CCOC1=O
HLC RCSB PDB D3W065 297.7 Da LogP 1.93 TPSA 64.6 ✓ Ro5 ✓ Clean c1cc(ccc1OCCCC(=O)N[C@H]2CCOC2=O)Cl
HTF RCSB PDB D3W065 227.3 Da LogP 1.78 TPSA 55.4 ✓ Ro5 ✓ Clean CCCCCCCC(=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.