Protein target profile

KP13_04902

TonB-dependent siderophore receptor

Genome: KpKP13 Gene: AHE45262.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GLH7
Length 731
Pocket druggability 0.997
Direct ligand evidence 0 59 total records
Functional annotation 0 EC 6 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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
1.4% 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
OuterMembrane

Structure confidence

ColabFold pLDDT
91.83 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 0.997
Structure A0A0H3GLH7
Pocket Pocket 3
P2Rank 0.991
Structure A0A0H3GLH7
Pocket Pocket 1
ColabFold model
FPocket 0.982 · Pocket 28
P2Rank 0.991 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 68 / 4744 genomes with a hit
Prevalence 1.4%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MDMKKRLWVLHPLLLASTLPALAAQSDEDSIIVSANRTHRTVAEMAQTTWVIEGQEIEQQVQGGKEFKDVLAQLIPGIDVSSQGRTNYGMNMRGRAIVVLIDGVRLNSSRTDSRQLDAIDPFNIEHIEVISGATSLYGGGSTGGLINIVTKKGQQDRQVDLEVGSKSGFANSNDHDERVAAAVSGGTDHASGRLSVAYQRFGGWYDGNNDALILDNTQTGLQHSERLDVMGTGTIEIDDNRQLQLVTQYYKSQGDDDYGLWLGKNMSAVTSGGKAYTTDGLNSDRIPGTERHLISLQYSDADFFGQNLVSQVYYRDESLTFYPFPTLTKGQVSSFSSSQQDTDQYGAKLTLNSQPLAGWDLTWGLDADHETFNANQMFFDLPQSMASGGLHNESIYTTGRYPGYSISNVAPFLQSSYDLNDIFTVSGGVRYQWTENRVDDFVGYAQQQDIANGKARSADAIKGGKTDYDNFLFNAGIVAHLTERQQTWFNFSQGVELPDPGKYYGIGKYGAAVNGHLPLISSVNVDDSPLQGIKVNSYELGWRYTGDNLRTQLAAYYSTSDKTIVVNRTDMTIDVQSDKRRIYGVEGAVDYFIPDSDWSVGGNFNVLKSQVQTDGRWQKWDVTLASPSKATAWVGWAPDPWSLRVQSQQVFDLSDAAGNKLEGYNTVDFIGSYALPVGKLTFSIENLLNEDYVTIWGQRAPLLYSPTYGSSSLYEYKGRGRTFGLNYALTF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • 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:0015891 The directed movement of siderophores, low molecular weight Fe(III)-chelating substances, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • GO:0015343 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: siderophore-iron(out) + H+(out) = siderophore-iron(in) + H+(in).
  • GO:0038023 Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
  • 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.

27 records
Show feature table
Start End DB Term Name
156 731 Gene3D G3DSA:2.40.170.20 -
156 731 InterPro IPR036942 TonB-dependent receptor-like, beta-barrel domain superfamily
21 154 FunFam G3DSA:2.170.130.10:FF:000011 TonB-dependent siderophore receptor
44 731 NCBIfam TIGR01783 TonB-dependent siderophore receptor
44 731 InterPro IPR010105 TonB-dependent siderophore receptor
1 23 SignalP_EUK SignalP-noTM SignalP-noTM
7 19 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
22 155 Gene3D G3DSA:2.170.130.10 -
22 155 InterPro IPR037066 TonB-dependent receptor, plug domain superfamily
48 731 CDD cd01347 ligand_gated_channel
1 23 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
1 23 Phobius SIGNAL_PEPTIDE Signal peptide region
158 731 FunFam G3DSA:2.40.170.20:FF:000007 Ferric aerobactin receptor
20 23 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
43 144 Pfam PF07715 TonB-dependent Receptor Plug Domain
43 144 InterPro IPR012910 TonB-dependent receptor, plug domain
1 6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
24 731 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
16 727 PANTHER PTHR30069 TONB-DEPENDENT OUTER MEMBRANE RECEPTOR
16 727 InterPro IPR039426 TonB-dependent receptor-like
29 731 SUPERFAMILY SSF56935 Porins
241 727 Pfam PF00593 TonB dependent receptor
241 727 InterPro IPR000531 TonB-dependent receptor-like, beta-barrel
714 731 ProSitePatterns PS01156 TonB-dependent receptor proteins signature 2.
714 731 InterPro IPR010917 TonB-dependent receptor, conserved site
1 36 ProSitePatterns PS00430 TonB-dependent receptor proteins signature 1.
1 36 InterPro IPR010916 TonB box, conserved site

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 #3
0.997
Likely same site as P2Rank 1 6.4 Å 40 shared residues 93% of smaller site
Unusual size
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Surrounding area
Site 2 FPocket #1
0.707
Likely same site as P2Rank 3 6.9 Å 17 shared residues 94% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 3 FPocket #9
0.477
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Surrounding area
Site 4 FPocket #12
0.332
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.991
Likely same site as FPocket 3 6.4 Å 40 shared residues 93% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.865
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Surrounding area
Site 3 P2Rank #3
0.517
Likely same site as FPocket 1 6.9 Å 17 shared residues 94% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.421
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Surrounding area
Site 5 P2Rank #5
0.232
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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_A0A0H3GLH7
AlphaFold DB full sequence Viewing
ColabFold KP13_04902
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.

59 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 9 records from similar proteins
Structural ligands 9 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
C8E PDB via homolog 306.4 Da · LogP 2.41 · TPSA 57.2 Open detail RCSB PDB
DPO PDB via homolog Detail RCSB PDB
FTT PDB via homolog Detail RCSB PDB
HEX PDB via homolog Detail RCSB PDB
LDA 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
C8E RCSB PDB P06129 306.4 Da LogP 2.41 TPSA 57.2 ✓ Ro5 ✓ Clean CCCCCCCCOCCOCCOCCOCCO
DPO RCSB PDB P06971 173.9 Da LogP -3.34 TPSA 135.6 ✓ Ro5 ✓ Clean [O-]P(=O)([O-])OP(=O)([O-])[O-]
FTT RCSB PDB P06971 244.4 Da LogP 3.74 TPSA 57.5 ✓ Ro5 ✓ Clean CCCCCCCCCCC[C@H](CC(=O)O)O
HEX RCSB PDB P06129 86.2 Da LogP 2.59 TPSA 0.0 ✓ Ro5 ✓ Clean CCCCCC
LDA RCSB PDB P06129 229.4 Da LogP 4.48 TPSA 23.1 ✓ Ro5 ✓ Clean CCCCCCCCCCCC[N+](C)(C)[O-]
MPG RCSB PDB P06129 356.5 Da LogP 4.92 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC/C=C\CCCCCCCCOC(=O)[C@@H](CO)O
MTN RCSB PDB P06129 264.4 Da LogP 1.82 TPSA 57.3 ✓ Ro5 ✓ Clean CC1(C=C(C(N1[O])(C)C)CSS(=O)(=O)C)C
OCT RCSB PDB P06129 114.2 Da LogP 3.37 TPSA 0.0 ✓ Ro5 ✓ Clean CCCCCCCC
OES RCSB PDB P06971 206.4 Da LogP 2.09 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCC[S@@](=O)CCO

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.