KpKP13 Protein target profile

putative tonB-dependent receptor

Accession: KP13_04484

Gene: AHE44358.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQG7
Length 701
Pocket druggability (P2Rank · AlphaFold DB model) 0.974
Direct ligand evidence 0 57 total records
Functional annotation 0 EC 3 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
1.5% 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.

Structure confidence

ColabFold pLDDT
92.43 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) 0.974
Structure A0A0H3GQG7
Pocket Pocket 1
Druggability (FPocket) 0.826
Structure A0A0H3GQG7
Pocket Pocket 10
ColabFold model
P2Rank 0.974 · Pocket 1
FPocket 0.809 · Pocket 3
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 71 / 4744 genomes with a hit
Prevalence 1.5%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MKILSVRHAALPALLLPLIAAAQAADEQTMVVTAAPTTVSELDTPAAVSVVNGDEMRQAAPRVNLSESLGAVPGLQVQNRQNYAQDLQLSIRGFGSRSTYGVRGLRIYVDGIPATMPDGQGQTSNIDIGSVDTIEVLRGPFSALYGNSSGGVINVTSQTGTQPPTVEASSYYGSFGTWHYGMKATGAVGDGSHAGDVDYTVSTNRFTTHGYRDHSGARKNLANARLGVRINDVSKLTLLLNSVDIKANDAGGLTADEWRDNPRQSPRGDQYNTRKNTRQTQAGLRYERQLSAQDDLSVMMYAGERETTQFQSIPRAPQLKPSHAGGVIDLTRHYQGIDTRLTHRGELLVPVTLTAGLDYENMSERRKGYENFVMVNGAPQYGEQGALRRNERNLMWNVDPYLQTQWQLTDKLSLDAGVRYSSVWFDSNDYYITPGNGDDSGDASYHKWLPAGSLKYALTDAWNVYLSAGRGFETPTINELSYRSDNQSGLNFGLKPSTNDTVEIGSKTRIGNGLFTAALFQTNTDNEIVVDSSSGGRTSYKNAGKTRRQGMELGLDQQFGESWRLKAAWTWLDATYRTNVCDDASCNGNRIPGIARNMGYASFGYQPEQGWYAGSDIRYMSDIMANDENTAKAPSWTVVGLTTGYKWSYGRMDMDLFGRIDNLFDREYVGSVIVNESNGRYYEPAPGRNYGIGLNLAWRFE

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.

21 records
Show feature table
Start End DB Term Name
255 282 MobiDBLite mobidb-lite consensus disorder prediction
20 24 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
20 698 SUPERFAMILY SSF56935 Porins
48 698 CDD cd01347 ligand_gated_channel
1 8 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 24 SignalP_EUK SignalP-noTM SignalP-noTM
25 701 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
9 19 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
179 697 Gene3D G3DSA:2.40.170.20 -
179 697 InterPro IPR036942 TonB-dependent receptor-like, beta-barrel domain superfamily
41 152 Pfam PF07715 TonB-dependent Receptor Plug Domain
41 152 InterPro IPR012910 TonB-dependent receptor, plug domain
265 282 MobiDBLite mobidb-lite consensus disorder prediction
1 24 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
1 24 Phobius SIGNAL_PEPTIDE Signal peptide region
251 696 Pfam PF00593 TonB dependent receptor
251 696 InterPro IPR000531 TonB-dependent receptor-like, beta-barrel
14 696 PANTHER PTHR30069 TONB-DEPENDENT OUTER MEMBRANE RECEPTOR
14 696 InterPro IPR039426 TonB-dependent receptor-like
20 163 Gene3D G3DSA:2.170.130.10 -
20 163 InterPro IPR037066 TonB-dependent receptor, plug domain superfamily

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

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.974
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Surrounding area
Pocket 2 P2Rank #2
0.951
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Surrounding area
Pocket 3 P2Rank #3
0.901
Likely same site as FPocket 2 2.6 Å 24 shared residues 71% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.321
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Surrounding area
Pocket 5 P2Rank #5
0.224
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #10
0.826
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Surrounding area
Pocket 2 FPocket #2
0.698 Unusual size
Likely same site as P2Rank 3 2.6 Å 24 shared residues 71% of smaller site
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Surrounding area
Pocket 3 FPocket #45
0.693
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Surrounding area
Pocket 4 FPocket #27
0.601
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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_A0A0H3GQG7
AlphaFold DB full sequence Viewing
ColabFold KP13_04484
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
6L0 PDB via homolog 598.7 Da · LogP 0.63 · TPSA 208.9 Open detail RCSB PDB
C8E PDB via homolog Detail RCSB PDB
FLC PDB via homolog Detail RCSB PDB
FTT PDB via homolog Detail RCSB PDB
HTO 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
6L0 RCSB PDB Q9I116 598.7 Da LogP 0.63 TPSA 208.9 2 viol. ✓ Clean C1CCNC(=O)CCC(=O)N(CCCCCNC(=O)CCC(=O)N(C/C=C/CC…
C8E RCSB PDB D0CAH3 306.4 Da LogP 2.41 TPSA 57.2 ✓ Ro5 ✓ Clean CCCCCCCCOCCOCCOCCOCCO
FLC RCSB PDB P13036 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
FTT RCSB PDB Q9I116 244.4 Da LogP 3.74 TPSA 57.5 ✓ Ro5 ✓ Clean CCCCCCCCCCC[C@H](CC(=O)O)O
HTO RCSB PDB P13036 148.2 Da LogP -0.11 TPSA 60.7 ✓ Ro5 ✓ Clean CCCC[C@H]([C@@H](CO)O)O
LDA RCSB PDB P13036 229.4 Da LogP 4.48 TPSA 23.1 ✓ Ro5 ✓ Clean CCCCCCCCCCCC[N+](C)(C)[O-]
OES RCSB PDB P17315 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.