Protein target profile
KP13_05561
Phosphoglycerate transport system sensor protein pgtB
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
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
- 0.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- N
- DEG identity (%)
- 0.0 Higher values support similarity to known essential genes.
Localization
- Localization
- CytoplasmicMembrane
Structure confidence
- ColabFold pLDDT
- 83.02 0-100 confidence; >70 supports local structural interpretation.
Binding-site evidence
AlphaFold DB / UniProt modelThe selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.
Cross-references
External database identifiers for this protein, its structures, ligands, and metabolic reactions.
Sequence
Sequence
Primary amino-acid sequence viewer.
MLQRLRQISISSSLRGAFLTGALLTLIVSSVSLYSWHEQSSQIRYSLDEYFPRIHAAFLIEGNLNLVVDQLNEFLLAPNTTVRLQLRNQIIQHLDKIERLSQGLSPAERQQLGVILQDSRALLAELDRVLYNMFLVREKVGELAARIDWLHDDFTTELNSLVQDFTWQQGTLLDQIEARQGDARQYLKRAREVQNEQQQVYTLARIENQIVDDLRDRLNELKSGNDDGMLVETHIRYLENLKKTADENIRALDDWPSTITLRQTIDELLEIGMVKNNMPDTMRDYVSAQKALVEASRSREATLGRFRTLLEAQLGSSHQQMQMFNQRMAQIVRVSGGLILVATLLALLLAWGLNHYFIRSRLVKRFSALNQAVVQIGLGRTEATIPVYGRDELGRIAGLLRHTLGQLNAQKQQLEQEIGERKAIEADLRATQDELIQTAKLAVVGQTMTTLAHEINQPLNALSMYLFTAGRAIEQGQAEQARMTLSKAEGLINRIDAIIRSLRQFTRRAELETPLHPVDLRQTFTVAWELLAMRHKPQQGTLVIPDDTVWIQGDEVRVHQVLVNVLSNALDACPHAAQITVSWQIQGGRLCVLIADNGPGWPAALLPSLLKPFTTSKTVGLGIGLSICVSLMTQMEGALRLASTFTRSACVVLEFNLTDVKDVE
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Enzyme Commission (EC)
1Gene Ontology (GO)
5- GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
- GO:0000155 Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
- GO:0007165 The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
- GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
- GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 419 | 506 | Gene3D | G3DSA:1.10.287.130 | - |
| 1 | 403 | PIRSF | PIRSF037119 | HK_PgtB |
| 1 | 403 | InterPro | IPR017116 | Signal transduction histidine kinase, PgtB |
| 398 | 661 | PIRSF | PIRSF037119 | HK_PgtB |
| 398 | 661 | InterPro | IPR017116 | Signal transduction histidine kinase, PgtB |
| 439 | 507 | SUPERFAMILY | SSF47384 | Homodimeric domain of signal transducing histidine kinase |
| 439 | 507 | InterPro | IPR036097 | Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily |
| 553 | 659 | SMART | SM00387 | HKATPase_4 |
| 553 | 659 | InterPro | IPR003594 | Histidine kinase/HSP90-like ATPase |
| 558 | 655 | CDD | cd00075 | HATPase |
| 510 | 655 | SUPERFAMILY | SSF55874 | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase |
| 510 | 655 | InterPro | IPR036890 | Histidine kinase/HSP90-like ATPase superfamily |
| 29 | 33 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. |
| 360 | 412 | ProSiteProfiles | PS50885 | HAMP domain profile. |
| 360 | 412 | InterPro | IPR003660 | HAMP domain |
| 1 | 16 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. |
| 15 | 37 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. |
| 441 | 507 | CDD | cd00082 | HisKA |
| 441 | 507 | InterPro | IPR003661 | Signal transduction histidine kinase, dimerisation/phosphoacceptor domain |
| 553 | 657 | Pfam | PF02518 | Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase |
| 553 | 657 | InterPro | IPR003594 | Histidine kinase/HSP90-like ATPase |
| 317 | 418 | Gene3D | G3DSA:6.10.340.10 | - |
| 360 | 412 | SMART | SM00304 | HAMP_11 |
| 445 | 508 | Pfam | PF00512 | His Kinase A (phospho-acceptor) domain |
| 445 | 508 | InterPro | IPR003661 | Signal transduction histidine kinase, dimerisation/phosphoacceptor domain |
| 34 | 333 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. |
| 357 | 408 | Pfam | PF00672 | HAMP domain |
| 357 | 408 | InterPro | IPR003660 | HAMP domain |
| 331 | 353 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. |
| 17 | 28 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. |
| 397 | 434 | Coils | Coil | Coil |
| 107 | 647 | PANTHER | PTHR43065 | SENSOR HISTIDINE KINASE |
| 1 | 33 | Phobius | SIGNAL_PEPTIDE | Signal peptide region |
| 443 | 511 | SMART | SM00388 | HisKA_10 |
| 443 | 511 | InterPro | IPR003661 | Signal transduction histidine kinase, dimerisation/phosphoacceptor domain |
| 515 | 662 | Gene3D | G3DSA:3.30.565.10 | - |
| 515 | 662 | InterPro | IPR036890 | Histidine kinase/HSP90-like ATPase superfamily |
| 334 | 357 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. |
| 358 | 664 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. |
| 450 | 659 | ProSiteProfiles | PS50109 | Histidine kinase domain profile. |
| 450 | 659 | InterPro | IPR005467 | Histidine kinase 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.
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 · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
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_A0A0H3GTK9
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
KP13_05561
|
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 |
|---|---|---|---|---|---|---|
| EMC RCSB PDB | Q9X180 | 229.7 Da LogP 0.97 TPSA 0.0 | ✓ Ro5 | ✓ Clean |
CC[Hg+]
|
|
| EMT RCSB PDB | Q9X180 | 382.8 Da LogP 2.91 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
CC[Hg]Sc1ccccc1C(=O)O
|
|
| PG0 RCSB PDB | P71815 | 120.1 Da LogP -0.36 TPSA 38.7 | ✓ Ro5 | ✓ Clean |
COCCOCCO
|
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
|
| ZINC575419714 ZINC | 0.727 | 312.4 Da LogP 0.42 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCSCCOCCOCCO
|
| ZINC115163232 ZINC | 0.700 | 222.3 Da LogP 0.07 TPSA 57.2 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCCO
|
| 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
|
| 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
|
| ZINC116078641 ZINC | 0.583 | 222.2 Da LogP -0.80 TPSA 74.2 | ✓ Ro5 | ✓ Clean |
COC(=O)COCCOCCOCCO
|
| 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
|
| ZINC34764844 ZINC | 0.550 | 206.3 Da LogP 1.09 TPSA 36.9 | ✓ Ro5 | ✓ Clean |
CCCOCCOCCOCCOC
|
| ZINC5369059 ZINC | 0.548 | 274.3 Da LogP 3.23 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1Sc1ccccc1C(=O)O
|
| ZINC1644613 ZINC | 0.545 | 206.3 Da LogP 0.83 TPSA 47.9 | ✓ Ro5 | ✓ Clean |
CCCCOCCOCCOCCO
|
| ZINC1672344 ZINC | 0.545 | 230.3 Da LogP 3.54 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1Sc1ccccc1
|
| ZINC2675142 ZINC | 0.545 | 334.4 Da LogP 3.97 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1SCCSc1ccccc1C(=O)O
|
| ZINC2383745924 ZINC | 0.542 | 398.5 Da LogP -0.01 TPSA 94.1 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCC(CO)COCCOCCOCCOC
|
| ZINC5059317 ZINC | 0.541 | 240.3 Da LogP 2.34 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
CC[C@H](Sc1ccccc1C(=O)O)C(=O)O
|
| ZINC5059320 ZINC | 0.541 | 240.3 Da LogP 2.34 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
CC[C@@H](Sc1ccccc1C(=O)O)C(=O)O
|
| ZINC7262012 ZINC | 0.541 | 210.3 Da LogP 3.28 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
CCCCSc1ccccc1C(=O)O
|
| ZINC3122032 ZINC | 0.529 | 256.2 Da LogP 1.01 TPSA 111.9 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1SC(C(=O)O)C(=O)O
|
| ZINC2584162 ZINC | 0.528 | 210.3 Da LogP 3.13 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
CC(C)CSc1ccccc1C(=O)O
|
| ZINC3375023 ZINC | 0.528 | 210.3 Da LogP 2.07 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
CC(=O)CSc1ccccc1C(=O)O
|
| ZINC19263534 ZINC | 0.526 | 224.3 Da LogP 3.67 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
CCCCCSc1ccccc1C(=O)O
|
| ZINC115086873 ZINC | 0.524 | 209.2 Da LogP -1.08 TPSA 83.2 | ✓ Ro5 | ✓ Clean |
NOCCOCCOCCOCCO
|
| ZINC140264883 ZINC | 0.524 | 223.3 Da LogP -0.43 TPSA 72.2 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCON
|
| ZINC146143823 ZINC | 0.524 | 237.3 Da LogP -1.00 TPSA 83.2 | ✓ Ro5 | ✓ Clean |
NCCOCCOCCOCCOCCO
|
| ZINC5024003 ZINC | 0.524 | 251.3 Da LogP -0.34 TPSA 72.2 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCN
|
| ZINC83253927 ZINC | 0.524 | 400.5 Da LogP 0.68 TPSA 73.8 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCOCCOCCS
|
| ZINC83253930 ZINC | 0.524 | 224.3 Da LogP 0.61 TPSA 36.9 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCS
|
| ZINC90741447 ZINC | 0.524 | 298.4 Da LogP -0.01 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCS
|
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.