Protein target profile

KP13_01078

Penicillin-binding protein activator LpoA

Genome: KpKP13 Gene: lpoA AHE42529.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GTM6
Length 714
Pocket druggability 0.096
Direct ligand evidence 0 51 total records
Functional annotation 0 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
1.9% 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
Unknown

Structure confidence

ColabFold pLDDT
75.87 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 0.096
Structure A0A0H3GTM6
Pocket Pocket 48
P2Rank 0.65
Structure A0A0H3GTM6
Pocket Pocket 1
ColabFold model
FPocket 0.35 · Pocket 43
P2Rank 0.217 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 91 / 4744 genomes with a hit
Prevalence 1.9%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MSIEPKKYHWTLMVPSTFLRSKPARCLPVLLATLIFAGCGTHTQDQSAAFMQGTSQANSSFYLQQMQQSTNDSKTNWQLLAIRALLQEGKKQQAIDLFNQLPANLNSTQAREQSLLAVEVKLAQNDYQAARNLLAKIDPTNLEQPQQARYWQAQIDASQGKPSLTLLRALIAQQPLLSDAKQRQKNINATWQALTSMPQDQANALVINADENILQGWLDLQRMWFDSRNDPTLLKAGVKDWQTRYPQNPGAKMLPTALVNMQNYKPASINKIALFLPLNGQASIFGRTIQQGFEAAKNGAPSVTGSAVPAQVAQAANVSGNDDVVSPSQAEISDLTATGSRADPVQAPTQDQAAPAAEPAAQAPATSTTPQTTASPATQPVTAPAAQPQPVVATAANPSAELKIYDTTSQPISQLLAQAQQDGATLVVGPLLKENVEEVIKSNTPLNVLALNQPEKVESRANLCYFALSPEDEARDAARHIHQQGKQTPLLLVPRGALGDRVVSAFADEWLKLGGASVLQQRFGSTAELRAGVNGGGGIALSGTPVSTLPSAQNSILGSADEMPVSSGGSVDAAYILATPEQIAYIKPMIAMRNGSQSNVTLYASSRSAQGTAGPDFRLEMEGLQYSEIPMLAGSNPSLMQQALSAVRNDYSLARLYAMGADAWSLANHFTQMRQTPGFELNGNTGDLTANQDCVINRKLSWLKYQQGKIVPAS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0005515 Binding to a protein.
  • GO:0031241 The leaflet of a outer cell membrane that faces the periplasm, including any protein embedded in, attached to, or peripherally associated with it.
  • GO:0030234 A molecular function regulator that modulates a catalytic activity.
  • GO:0009252 The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.
  • GO:0008360 Any process that modulates the surface configuration of a cell.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
18 708 Hamap MF_01890 Penicillin-binding protein activator LpoA [lpoA].
18 708 InterPro IPR007443 Penicillin-binding protein activator LpoA
269 375 Gene3D G3DSA:3.40.50.2300 -
271 712 SUPERFAMILY SSF53822 Periplasmic binding protein-like I
271 712 InterPro IPR028082 Periplasmic binding protein-like I
1 57 Phobius SIGNAL_PEPTIDE Signal peptide region
469 703 Gene3D G3DSA:3.40.50.2300 -
394 701 Gene3D G3DSA:3.40.50.2300 -
160 268 Gene3D G3DSA:1.25.40.650 -
26 39 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 25 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
36 159 Gene3D G3DSA:1.25.40.10 Tetratricopeptide repeat domain
36 159 InterPro IPR011990 Tetratricopeptide-like helical domain superfamily
319 347 MobiDBLite mobidb-lite consensus disorder prediction
1 48 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
319 394 MobiDBLite mobidb-lite consensus disorder prediction
53 298 Pfam PF04348 LppC putative lipoprotein
53 298 InterPro IPR007443 Penicillin-binding protein activator LpoA
395 708 Pfam PF04348 LppC putative lipoprotein
395 708 InterPro IPR007443 Penicillin-binding protein activator LpoA
362 385 MobiDBLite mobidb-lite consensus disorder prediction
395 703 CDD cd06339 PBP1_YraM_LppC_lipoprotein-like
58 714 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
13 714 PANTHER PTHR38038 PENICILLIN-BINDING PROTEIN ACTIVATOR LPOA
13 714 InterPro IPR007443 Penicillin-binding protein activator LpoA
40 57 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.

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 · P2Rank

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

Site 1 P2Rank #1
0.65
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Surrounding area
Site 2 P2Rank #2
0.389
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Surrounding area
Site 3 P2Rank #3
0.168
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Surrounding area
Site 4 P2Rank #4
0.125
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Surrounding area
Site 5 P2Rank #5
0.069
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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_A0A0H3GTM6
AlphaFold DB full sequence Viewing
ColabFold KP13_01078
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.

51 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 1 records from similar proteins
Structural ligands 1 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
GSH PDB via homolog 307.3 Da · LogP -2.21 · TPSA 158.8 Open detail RCSB PDB
ZINC3830891 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC3830892 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC3830893 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC3830894 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
GSH RCSB PDB Q7P0B4 307.3 Da LogP -2.21 TPSA 158.8 1 viol. ✓ Clean C(CC(=O)N[C@@H](CS)C(=O)NCC(=O)O)[C@@H](C(=O)O)N

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.