KpATCC43816 Protein target profile
phosphonate metabolism transcriptional regulatorPhnF
Accession: VK055_2966
Promising target candidate with multiple supporting evidence streams.
Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.
Main supporting evidence
Risks to review
Evidence coverage
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
- 1.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- N
- DEG identity (%)
- 29.185 Higher values support similarity to known essential genes.
Structure confidence
- ColabFold pLDDT
- 85.34 0-100 confidence; >70 supports local structural interpretation.
Binding-site evidence
AlphaFold DB / UniProt modelP2Rank'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.
Sequence
Primary amino-acid sequence viewer.
MHLSRHPTSYPTRYQEIAARLEQELRHHYRCGDYLPAEQQLATRFDVNRHTLRRDIDQLVERGWVQRRQGVGVLVLMRPIDYPLNAQARFSQNLLEQGSDPTSEKLLSVLRPASAHVAEAFGINEGENVIHLRTLRRVNGVALCLIDHYFADLRFWPVLQTFSHGSLHDLLRDRLDVELTRVRTKISARRAQAKESKLLEIPNMAPLLCVRTLNSREGESLTAEYSVSLTRADMIEFTMEH
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Subcellular localization
- Localization
- Cytoplasmic
Gene Ontology (GO)
3- GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
- 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.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 49 | 65 | PRINTS | PR00035 | GntR bacterial regulatory protein HTH signature |
| 11 | 78 | ProSiteProfiles | PS50949 | GntR-type HTH domain profile. |
| 11 | 78 | InterPro | IPR000524 | Transcription regulator HTH, GntR |
| 63 | 240 | SUPERFAMILY | SSF64288 | Chorismate lyase-like |
| 63 | 240 | InterPro | IPR028978 | Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily |
| 96 | 236 | SMART | SM00866 | UTRA_2 |
| 96 | 236 | InterPro | IPR011663 | UbiC transcription regulator-associated |
| 12 | 76 | Gene3D | G3DSA:1.10.10.10 | - |
| 12 | 76 | InterPro | IPR036388 | Winged helix-like DNA-binding domain superfamily |
| 96 | 235 | Pfam | PF07702 | UTRA domain |
| 96 | 235 | InterPro | IPR011663 | UbiC transcription regulator-associated |
| 12 | 75 | CDD | cd07377 | WHTH_GntR |
| 12 | 75 | InterPro | IPR000524 | Transcription regulator HTH, GntR |
| 8 | 83 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain |
| 8 | 83 | InterPro | IPR036390 | Winged helix DNA-binding domain superfamily |
| 35 | 49 | PRINTS | PR00035 | GntR bacterial regulatory protein HTH signature |
| 35 | 49 | InterPro | IPR000524 | Transcription regulator HTH, GntR |
| 49 | 65 | InterPro | IPR000524 | Transcription regulator HTH, GntR |
| 17 | 75 | SMART | SM00345 | gntr3 |
| 17 | 75 | InterPro | IPR000524 | Transcription regulator HTH, GntR |
| 14 | 75 | Pfam | PF00392 | Bacterial regulatory proteins, gntR family |
| 14 | 75 | InterPro | IPR000524 | Transcription regulator HTH, GntR |
| 83 | 241 | Gene3D | G3DSA:3.40.1410.10 | - |
| 83 | 241 | InterPro | IPR028978 | Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily |
| 11 | 240 | PANTHER | PTHR44846 | MANNOSYL-D-GLYCERATE TRANSPORT/METABOLISM SYSTEM REPRESSOR MNGR-RELATED |
| 6 | 241 | NCBIfam | TIGR02325 | phosphonate metabolism transcriptional regulator PhnF |
| 6 | 241 | InterPro | IPR012702 | Phosphonate C-P lyase system, transcriptional regulator PhnF |
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.
How colors and pocket overlays are used
Pocket details Inspect a specific pocket, or open the full viewer
- Method
- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
Selecting a pocket opens its details and centers the viewer without clearing other active layers. Use Focus this pocket when you want to hide the rest; use Surface for the wider residue environment.
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
All structural evidence
Structural evidence
0 + 2Experimental 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_A0A0H3GL57
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_2966
|
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.
Structural ligand evidence is available for this target.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.
No PDB structure with a co-crystallized ligand found for this exact protein.
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.
Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL bioactivity data found for this exact protein.
Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL hits found through similar proteins.
Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).
No virtual-screening candidates for this protein.
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.