Genome KpATCC43816

Protein target profile

tonB dependent receptor family protein

Accession: VK055_4427

Gene: AIK82970.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GS89
Length 787
Pocket druggability (P2Rank) 0.993
Direct ligand evidence 0 57 total records
Functional annotation 0 EC 3 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 (%)
26.953 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
89.14 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank'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.

Druggability (P2Rank) 0.993
Structure A0A0H3GS89
Pocket Pocket 1
Druggability (FPocket) 0.979
Structure A0A0H3GS89
Pocket Pocket 1
ColabFold model
P2Rank 0.994 · Pocket 1
FPocket 0.903 · Pocket 30
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 23 / 4744 genomes with a hit
Prevalence 0.5%

Cross-references

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

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MYKSTPSAAWCKKRLLVTSLFAAIYQTSAIAADTSAVSGEAVDDTSEQMTVTAPAPVQKAGSEHSISARELENKGANDFGSIMRYEPLISATGASGGSGNGKSGFDRGGYTGYNIRGMESNRVGIDVDGIAQPNATGRGYVGRAGLNTFGIGRDYIDPYMYGSVDIQSGATSTETANSAIGGNVSFRPKSADDYLRPGKTSAFGYRSGYDSADRNWHNGVTVAGGDEFLRGILVYSRRDGQETENNSGTVDAYPANWHSDAFLASGIWQPNDEHKLTSTFDYYHKTNHTHYDTWDSSGNSTIGTANQTSQTRRWGLSLKDDWTPMNDYLDSVSTKIYYQHTEAHDWTYMPDSITRKMQTVNSNYDTDTWGLQTALAKTLGRHDLSAGFNASTSKTQRPFSQSPIPSVYSEIMQPEADSRSYTLGGFVQDKINFDLDSHNFAVIPGVRVVHQSTKPENLSDLAANSSVLSESSVANLYGKNSDTQVLPSLTFQYDLTPRLMTYLQYQRGAQFPNASQLYGSWNLGSSYAGSQQYALIGNTDLKTETSDNLEWGLKGEVTEGITLRTALFYNSYKNFIAYTRYTRANNPGQFTNVPSNIYTIYQAENRDKAYIYGGEISTKFNFGTWFEQVDGLSATLALGYSEGKSKSSYSGDKYVDLDSVAPMKAIVGVAWDDPAKRYGTALTATFVKGKQATATNRESYSNSGSAITDASSDYMRVPGYGMLDWTAYWQVAKNVRLNGGVYNLTDRKYWDYLSSRNIETGTNQDANDKALAVMPGRTWQLGVNVDF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Subcellular localization

Localization
OuterMembrane

Gene Ontology (GO)

3
  • GO:0009279 A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
  • GO:0015344 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: siderophore-iron(ferrioxamine)(out) + H+(out) = siderophore-iron(ferrioxamine)(in) + H+(in).
  • GO:0044718 The directed movement of siderophores, low molecular weight Fe(III)-chelating substances, from one side of a membrane to the other, by means of some agent such as a transporter or pore.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
60 182 Pfam PF07715 TonB-dependent Receptor Plug Domain
60 182 InterPro IPR012910 TonB-dependent receptor, plug domain
65 787 CDD cd01347 ligand_gated_channel
357 785 Pfam PF00593 TonB dependent receptor
357 785 InterPro IPR000531 TonB-dependent receptor-like, beta-barrel
32 787 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 31 SignalP_EUK SignalP-noTM SignalP-noTM
17 787 PANTHER PTHR30069 TONB-DEPENDENT OUTER MEMBRANE RECEPTOR
17 787 InterPro IPR039426 TonB-dependent receptor-like
27 31 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 14 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
201 787 Gene3D G3DSA:2.40.170.20 -
201 787 InterPro IPR036942 TonB-dependent receptor-like, beta-barrel domain superfamily
15 26 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
59 198 Gene3D G3DSA:2.170.130.10 -
59 198 InterPro IPR037066 TonB-dependent receptor, plug domain superfamily
1 31 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
1 31 Phobius SIGNAL_PEPTIDE Signal peptide region
43 787 SUPERFAMILY SSF56935 Porins

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

Pocket 1 P2Rank #1
0.993
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.928
Likely same site as FPocket 1 2.4 Å 35 shared residues 92% of smaller site
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.915
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.888
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.8
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.979 Unusual size
Likely same site as P2Rank 2 2.4 Å 35 shared residues 92% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #47
0.936 Unusual size
Show in viewer
Surrounding area
Pocket 3 FPocket #46
0.81
Show in viewer
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_A0A0H3GS89
AlphaFold DB full sequence Viewing
ColabFold VK055_4427
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.

57 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
8SW PDB via homolog 692.6 Da · LogP -1.77 · TPSA 296.0 Open detail RCSB PDB
8T2 PDB via homolog Detail RCSB PDB
95B PDB via homolog Detail RCSB PDB
C8E PDB via homolog Detail RCSB PDB
EB4 PDB via homolog Detail RCSB PDB

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
8SW RCSB PDB Q05098 692.6 Da LogP -1.77 TPSA 296.0 3 viol. Alert C#CCNC(=O)C(CNC(=O)C(CNC(=O)CNC(=O)c1cccc(c1O)O…
8T2 RCSB PDB Q05098 624.6 Da LogP 1.95 TPSA 237.8 2 viol. Alert c1cc(c(c(c1)O)O)C(=O)NCCCC[C@@H](C(=O)NCCCCNC(=…
95B RCSB PDB Q05098 418.4 Da LogP 1.29 TPSA 176.4 1 viol. Alert c1cc(c(c(c1)O)O)C(=O)NCCCC[C@@H](C(=O)O)NC(=O)c…
C8E RCSB PDB Q9K0U9 306.4 Da LogP 2.41 TPSA 57.2 ✓ Ro5 ✓ Clean CCCCCCCCOCCOCCOCCOCCO
EB4 RCSB PDB Q05098 669.6 Da LogP -0.74 TPSA 287.6 3 viol. Alert c1cc(c(c(c1)O)O)C(=O)N[C@H]2COC(=O)[C@H](COC(=O…
LP5 RCSB PDB Q05098 711.9 Da LogP 4.91 TPSA 212.3 2 viol. ✓ Clean CCCCCCCCCCC[C@H](CC(=O)N[C@@H]1[C@H]([C@@H]([C@…
OWT RCSB PDB Q05098 963.0 Da LogP 1.10 TPSA 299.6 3 viol. Alert CC(=O)NCC1CN(C(=O)O1)c2ccc(c(c2)F)N3CCN(CC3)C(=…

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.