KpATCC43816 Protein target profile
bacterial regulatory helix-turn-helix, lysR family protein
Accession: VK055_3414
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
- 0.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- N
- DEG identity (%)
- 38.889 Higher values support similarity to known essential genes.
Structure confidence
- ColabFold pLDDT
- 93.72 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.
MQLRFFCQVALRGSVSRAADDLFRTQSAITRAIRDLEAALNVTLFERHYSGMVPTEYGKCILPRARRAIDDLQAIPALLQKHHTRSSGPLADAGWLFNTRRLAIFIQLYHVNHTQTVAQQLGITQPAVSAALKVLEKGADSALFRRTPEGVRPTPAAELLYPPVSRALNELENIWSDLAARRGVLEGTVRIGALPLSRTRLLPSAIAAFLAQHPGITLMTNESPYESLVADMRAGNIDFIIGALRQDEDLPDLCSEALFEEDMLILLRNNHPLLRHPDPRSQLATAQWVLPRANAPARNLLDKAFVTLGLPLPQPTVETGDAAMVRGLLQGSDMLAAVSASQMRFETDNGLLSVLPVPLPDTTRRIGLTFRAGSLPSPATQALLRFIYQQVQDGAV
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Subcellular localization
- Localization
- Cytoplasmic
Gene Ontology (GO)
4- 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:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
- GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
- GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 97 | 184 | Gene3D | G3DSA:1.10.10.10 | - |
| 97 | 184 | InterPro | IPR036388 | Winged helix-like DNA-binding domain superfamily |
| 100 | 158 | Pfam | PF00126 | Bacterial regulatory helix-turn-helix protein, lysR family |
| 100 | 158 | InterPro | IPR000847 | Transcription regulator HTH, LysR |
| 2 | 59 | Pfam | PF00126 | Bacterial regulatory helix-turn-helix protein, lysR family |
| 2 | 59 | InterPro | IPR000847 | Transcription regulator HTH, LysR |
| 1 | 18 | Phobius | SIGNAL_PEPTIDE | Signal peptide region |
| 2 | 76 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain |
| 2 | 76 | InterPro | IPR036390 | Winged helix DNA-binding domain superfamily |
| 2 | 89 | PANTHER | PTHR30419 | HTH-TYPE TRANSCRIPTIONAL REGULATOR YBHD |
| 1 | 55 | ProSiteProfiles | PS50931 | LysR-type HTH domain profile. |
| 1 | 55 | InterPro | IPR000847 | Transcription regulator HTH, LysR |
| 97 | 154 | ProSiteProfiles | PS50931 | LysR-type HTH domain profile. |
| 97 | 154 | InterPro | IPR000847 | Transcription regulator HTH, LysR |
| 1 | 4 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. |
| 184 | 390 | Pfam | PF03466 | LysR substrate binding domain |
| 184 | 390 | InterPro | IPR005119 | LysR, substrate-binding |
| 19 | 396 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. |
| 36 | 47 | PRINTS | PR00039 | LysR bacterial regulatory protein HTH signature |
| 36 | 47 | InterPro | IPR000847 | Transcription regulator HTH, LysR |
| 26 | 36 | PRINTS | PR00039 | LysR bacterial regulatory protein HTH signature |
| 26 | 36 | InterPro | IPR000847 | Transcription regulator HTH, LysR |
| 15 | 26 | PRINTS | PR00039 | LysR bacterial regulatory protein HTH signature |
| 15 | 26 | InterPro | IPR000847 | Transcription regulator HTH, LysR |
| 5 | 13 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. |
| 188 | 395 | Gene3D | G3DSA:3.40.190.290 | - |
| 14 | 18 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. |
| 92 | 207 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain |
| 92 | 207 | InterPro | IPR036390 | Winged helix DNA-binding domain superfamily |
| 185 | 393 | SUPERFAMILY | SSF53850 | Periplasmic binding protein-like II |
| 1 | 76 | Gene3D | G3DSA:1.10.10.10 | - |
| 1 | 76 | InterPro | IPR036388 | Winged helix-like DNA-binding domain superfamily |
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 · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
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_A0A0H3GXK9
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_3414
|
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.
| Ligand | Source crystal | UniProt (homolog) | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| 1PS RCSB PDB | Q8NP91 | 201.2 Da LogP -0.09 TPSA 61.1 | ✓ Ro5 | ✓ Clean |
c1cc[n+](cc1)CCCS(=O)(=O)[O-]
|
|
| AKG RCSB PDB | P73862 | 146.1 Da LogP -0.50 TPSA 91.7 | ✓ Ro5 | ✓ Clean |
C(CC(=O)O)C(=O)C(=O)O
|
|
| FOR RCSB PDB | Q8NP91 | 30.0 Da LogP -0.18 TPSA 17.1 | ✓ Ro5 | ✓ Clean |
C=O
|
|
| PEO RCSB PDB | Q8NP91 | 34.0 Da LogP 0.02 TPSA 40.5 | ✓ Ro5 | ✓ Clean |
OO
|
|
| PEU RCSB PDB | Q7WT50 | 1221.5 Da LogP 0.06 TPSA 269.4 | 2 viol. | ✓ Clean |
COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO…
|
|
| SAL RCSB PDB | Q7WT50 | 138.1 Da LogP 1.09 TPSA 57.5 | ✓ Ro5 | ✓ Clean |
c1ccc(c(c1)C(=O)O)O
|
|
| SKM RCSB PDB | Q8Y9N7 | 174.2 Da LogP -1.52 TPSA 98.0 | ✓ Ro5 | ✓ Clean |
C1[C@H]([C@@H]([C@@H](C=C1C(=O)O)O)O)O
|
|
| TSU RCSB PDB | P94678 | 172.2 Da LogP 1.24 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
Cc1ccc(cc1)S(=O)(=O)O
|
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).
| Ligand | Tanimoto | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|
| ZINC1580161 ZINC | 1.000 | 208.3 Da LogP -0.33 TPSA 57.2 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCO
|
| ZINC16052118 ZINC | 1.000 | 340.4 Da LogP -0.28 TPSA 84.8 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCOCCO
|
| ZINC16052257 ZINC | 1.000 | 384.5 Da LogP -0.26 TPSA 94.1 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC34317654 ZINC | 1.000 | 472.6 Da LogP -0.23 TPSA 112.5 | 1 viol. | ✓ Clean |
COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC44076059 ZINC | 1.000 | 428.5 Da LogP -0.24 TPSA 103.3 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC5210101 ZINC | 1.000 | 252.3 Da LogP -0.31 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCO
|
| ZINC5997860 ZINC | 1.000 | 296.4 Da LogP -0.29 TPSA 75.6 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCO
|
| ZINC34564963 ZINC | 0.900 | 248.3 Da LogP 2.91 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
Cc1ccc(-c2ccc(S(=O)(=O)O)cc2)cc1
|
| ZINC575419714 ZINC | 0.727 | 312.4 Da LogP 0.42 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCSCCOCCOCCO
|
| ZINC6093151 ZINC | 0.722 | 238.2 Da LogP 0.18 TPSA 108.7 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)c1ccc(S(=O)(=O)O)cc1
|
| ZINC115163232 ZINC | 0.700 | 222.3 Da LogP 0.07 TPSA 57.2 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCCO
|
| ZINC1866983 ZINC | 0.700 | 314.3 Da LogP 1.85 TPSA 108.7 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)c1ccc(-c2ccc(S(=O)(=O)O)cc2)cc1
|
| ZINC258837490 ZINC | 0.700 | 354.4 Da LogP 0.11 TPSA 84.8 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCOCCCO
|
| ZINC12501520 ZINC | 0.688 | 458.5 Da LogP -0.88 TPSA 123.5 | 1 viol. | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC1692489 ZINC | 0.688 | 222.3 Da LogP 0.33 TPSA 46.2 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOC
|
| ZINC3874716 ZINC | 0.688 | 414.5 Da LogP -0.90 TPSA 114.3 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC4283769 ZINC | 0.688 | 238.3 Da LogP -0.96 TPSA 77.4 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCO
|
| ZINC4521548 ZINC | 0.688 | 282.3 Da LogP -0.95 TPSA 86.6 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCO
|
| ZINC4530388 ZINC | 0.688 | 266.3 Da LogP 0.35 TPSA 55.4 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOC
|
| ZINC5178829 ZINC | 0.688 | 326.4 Da LogP -0.93 TPSA 95.8 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCO
|
| ZINC5178830 ZINC | 0.688 | 370.4 Da LogP -0.91 TPSA 105.1 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC5701172 ZINC | 0.688 | 310.4 Da LogP 0.36 TPSA 64.6 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCOC
|
| ZINC5997861 ZINC | 0.688 | 398.5 Da LogP 0.40 TPSA 83.1 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCOCCOCCOC
|
| ZINC575432150 ZINC | 0.667 | 344.4 Da LogP -0.89 TPSA 100.5 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCS(=O)(=O)CCOCCOCCO
|
| ZINC1857524240 ZINC | 0.652 | 207.3 Da LogP -0.75 TPSA 60.0 | ✓ Ro5 | ✓ Clean |
COCCNCCOCCOCCO
|
| ZINC400143 ZINC | 0.652 | 214.2 Da LogP 2.76 TPSA 57.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1-c1ccccc1O
|
| ZINC38392758 ZINC | 0.650 | 242.2 Da LogP 2.16 TPSA 74.6 | ✓ Ro5 | Alert |
O=C(C(=O)c1ccccc1O)c1ccccc1O
|
| ZINC404363 ZINC | 0.650 | 214.2 Da LogP 2.33 TPSA 57.5 | ✓ Ro5 | ✓ Clean |
O=C(c1ccccc1O)c1ccccc1O
|
| ZINC4521819 ZINC | 0.643 | 202.3 Da LogP 0.25 TPSA 58.3 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)CCC[n+]1ccccc1
|
| ZINC82548310 ZINC | 0.636 | 236.3 Da LogP 0.34 TPSA 88.5 | ✓ Ro5 | ✓ Clean |
CS(=O)(=O)c1ccc(S(=O)(=O)O)cc1
|
| ZINC105146 ZINC | 0.619 | 242.2 Da LogP 2.75 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1-c1ccccc1C(=O)O
|
| ZINC133397 ZINC | 0.619 | 246.3 Da LogP 3.14 TPSA 34.1 | ✓ Ro5 | ✓ Clean |
Cc1ccc(S(=O)(=O)c2ccc(C)cc2)cc1
|
| ZINC34279126 ZINC | 0.615 | 222.3 Da LogP 2.39 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
Cc1ccc2cc(S(=O)(=O)O)ccc2c1
|
| ZINC36294287 ZINC | 0.607 | 248.3 Da LogP 2.91 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
Cc1cccc(-c2ccc(S(=O)(=O)O)cc2)c1
|
| ZINC5650743 ZINC | 0.600 | 222.3 Da LogP 0.07 TPSA 57.2 | ✓ Ro5 | ✓ Clean |
CCOCCOCCOCCOCCO
|
| ZINC6403917 ZINC | 0.600 | 354.4 Da LogP 0.11 TPSA 84.8 | ✓ Ro5 | ✓ Clean |
CCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC2062 ZINC | 0.593 | 258.2 Da LogP 2.31 TPSA 83.8 | ✓ Ro5 | ✓ Clean |
O=C(Oc1ccccc1C(=O)O)c1ccccc1O
|
| ZINC4831627 ZINC | 0.593 | 370.5 Da LogP -0.21 TPSA 76.0 | ✓ Ro5 | ✓ Clean |
O=S(=O)(CC[n+]1ccccc1)CCS(=O)(=O)CC[n+]1ccccc1
|
| ZINC116078641 ZINC | 0.583 | 222.2 Da LogP -0.80 TPSA 74.2 | ✓ Ro5 | ✓ Clean |
COC(=O)COCCOCCOCCO
|
| ZINC1565641 ZINC | 0.583 | 214.3 Da LogP 2.23 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
CC(C)(C)c1ccc(S(=O)(=O)O)cc1
|
| ZINC1661217 ZINC | 0.583 | 234.3 Da LogP 2.60 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)c1ccc(-c2ccccc2)cc1
|
| ZINC1857790631 ZINC | 0.583 | 280.3 Da LogP -0.39 TPSA 83.5 | ✓ Ro5 | ✓ Clean |
COC(=O)CCOCCOCCOCCOCCO
|
| ZINC196151418 ZINC | 0.583 | 266.3 Da LogP -0.78 TPSA 83.5 | ✓ Ro5 | ✓ Clean |
COC(=O)COCCOCCOCCOCCO
|
| ZINC202958272 ZINC | 0.583 | 236.3 Da LogP -0.41 TPSA 74.2 | ✓ Ro5 | ✓ Clean |
COC(=O)CCOCCOCCOCCO
|
| ZINC34111591 ZINC | 0.583 | 207.3 Da LogP -1.06 TPSA 62.2 | ✓ Ro5 | ✓ Clean |
COCCOCCN(CCO)CCO
|
| ZINC642881862 ZINC | 0.583 | 324.4 Da LogP -0.38 TPSA 92.7 | ✓ Ro5 | ✓ Clean |
COC(=O)CCOCCOCCOCCOCCOCCO
|
| ZINC82369423 ZINC | 0.583 | 217.0 Da LogP 1.85 TPSA 57.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(O)c1Br
|
| ZINC95713705 ZINC | 0.583 | 264.0 Da LogP 1.70 TPSA 57.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(O)c1I
|
| ZINC1669673 ZINC | 0.577 | 206.7 Da LogP 1.90 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
Cc1ccc(S(=O)(=O)O)cc1Cl
|
| ZINC39194529 ZINC | 0.577 | 214.2 Da LogP 2.76 TPSA 57.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(-c2ccccc2)cc1O
|
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.