Protein target profile

KP13_05561

Phosphoglycerate transport system sensor protein pgtB

Genome: KpKP13 Gene: AHE44567.1 pgtB 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GTK9
Length 664
Pocket druggability 0.967
Direct ligand evidence 0 53 total records
Functional annotation 1 EC 5 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
0.5% 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 model

The 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.

FPocket 0.967
Structure A0A0H3GTK9
Pocket Pocket 59
P2Rank 0.87
Structure A0A0H3GTK9
Pocket Pocket 1
ColabFold model
FPocket 0.708 · Pocket 54
P2Rank 0.939 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 24 / 4744 genomes with a hit
Prevalence 0.5%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

Primary amino-acid sequence viewer.

MLQRLRQISISSSLRGAFLTGALLTLIVSSVSLYSWHEQSSQIRYSLDEYFPRIHAAFLIEGNLNLVVDQLNEFLLAPNTTVRLQLRNQIIQHLDKIERLSQGLSPAERQQLGVILQDSRALLAELDRVLYNMFLVREKVGELAARIDWLHDDFTTELNSLVQDFTWQQGTLLDQIEARQGDARQYLKRAREVQNEQQQVYTLARIENQIVDDLRDRLNELKSGNDDGMLVETHIRYLENLKKTADENIRALDDWPSTITLRQTIDELLEIGMVKNNMPDTMRDYVSAQKALVEASRSREATLGRFRTLLEAQLGSSHQQMQMFNQRMAQIVRVSGGLILVATLLALLLAWGLNHYFIRSRLVKRFSALNQAVVQIGLGRTEATIPVYGRDELGRIAGLLRHTLGQLNAQKQQLEQEIGERKAIEADLRATQDELIQTAKLAVVGQTMTTLAHEINQPLNALSMYLFTAGRAIEQGQAEQARMTLSKAEGLINRIDAIIRSLRQFTRRAELETPLHPVDLRQTFTVAWELLAMRHKPQQGTLVIPDDTVWIQGDEVRVHQVLVNVLSNALDACPHAAQITVSWQIQGGRLCVLIADNGPGWPAALLPSLLKPFTTSKTVGLGIGLSICVSLMTQMEGALRLASTFTRSACVVLEFNLTDVKDVE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene 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.

41 records
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.

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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 · FPocket

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

Site 1 FPocket #59
0.967
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Surrounding area
Site 2 FPocket #32
0.305
Likely same site as P2Rank 3 2.2 Å 7 shared residues 100% of smaller site
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.87
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Surrounding area
Site 2 P2Rank #2
0.073
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Surrounding area
Site 3 P2Rank #3
0.056
Likely same site as FPocket 32 2.2 Å 7 shared residues 100% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.031
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Surrounding area
Site 5 P2Rank #5
0.014
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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_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.

53 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 3 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
EMC PDB via homolog 229.7 Da · LogP 0.97 · TPSA 0.0 Open detail RCSB PDB
EMT PDB via homolog Detail RCSB PDB
PG0 PDB via homolog Detail RCSB PDB
ZINC1580161 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC16052118 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

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
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

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.