KpKP13 Protein target profile

putative 2-aminoethylphosphonate-binding periplasmic protein

Accession: KP13_00095

Gene: phnS AHE42018.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GV35
Length 355
Pocket druggability (P2Rank · AlphaFold DB model) 0.92
Direct ligand evidence 0 54 total records
Functional annotation 0 EC 4 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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.

Structure confidence

ColabFold pLDDT
89.83 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) 0.92
Structure A0A0H3GV35
Pocket Pocket 1
Druggability (FPocket) 0.374
Structure A0A0H3GV35
Pocket Pocket 3
ColabFold model
P2Rank 0.788 · Pocket 1
FPocket 0.4 · Pocket 6
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 22 / 4744 genomes with a hit
Prevalence 0.5%

Sequence

Primary amino-acid sequence viewer.

MKANLVYTRITNCDEAYTMKLSRLALLSLFALTSSPVWADGVVTVYSADGLHDGDNSWYQSQFAAFTKATGIKVQYVEGGSGAIVERLAKERTNPQADVLVTVPPFIQRAAKEQLLATFTPQGSAQIPGANDRYSPLVNNYLTFIYNGQLLKSAPASWQDLLDSRFKNKLQYSTPGQAGDGTAVMLQAFHSLGGKDAGFEYLGKLQANNVGPSASTGKLTALVNKGELYVANGDLQMNLSQMARNPNVKIFWPADDKGERSALALPYTIGLVQNGPNSENGKKLINFLLDKPAQSSVSARSWGLPVRSDVAPDDANFKAAKAALDGVKSWEPNWDDVAVSLSADIARWHKVTDSE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
Unknown

Gene Ontology (GO)

4
  • GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
  • GO:0030975 Binding to thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
  • GO:0030976 Binding to thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
  • GO:0015888 The directed movement of thiamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Thiamine is vitamin B1, a water soluble vitamin present in fresh vegetables and meats, especially liver.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
24 34 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 39 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
1 39 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
43 349 SUPERFAMILY SSF53850 Periplasmic binding protein-like II
21 351 PANTHER PTHR30006 THIAMINE-BINDING PERIPLASMIC PROTEIN-RELATED
1 23 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
65 321 Gene3D G3DSA:3.40.190.10 -
19 353 NCBIfam TIGR03227 2-aminoethylphosphonate ABC transporter substrate-binding protein
19 353 InterPro IPR017637 Putative 2-aminoethylphosphonate binding protein, ABC transporter
40 355 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
140 337 Gene3D G3DSA:3.40.190.10 -
1 39 Phobius SIGNAL_PEPTIDE Signal peptide region
56 294 Pfam PF01547 Bacterial extracellular solute-binding protein
56 294 InterPro IPR006059 Bacterial extracellular solute-binding protein
35 39 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

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

Pocket 1 P2Rank #1
0.92
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Surrounding area
Pocket 2 P2Rank #2
0.319
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.082
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.02
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #3
0.374
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_A0A0H3GV35
AlphaFold DB full sequence Viewing
ColabFold KP13_00095
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.

54 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 4 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
F6P PDB via homolog 260.1 Da · LogP -3.10 · TPSA 156.9 Open detail RCSB PDB
G6P PDB via homolog Detail RCSB PDB
S7P PDB via homolog Detail RCSB PDB
TPS PDB via homolog Detail RCSB PDB
ZINC100351924 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
F6P RCSB PDB A3N294 260.1 Da LogP -3.10 TPSA 156.9 1 viol. ✓ Clean C([C@@H]1[C@H]([C@@H]([C@](O1)(CO)O)O)O)OP(=O)(…
G6P RCSB PDB A3N294 260.1 Da LogP -3.10 TPSA 156.9 1 viol. ✓ Clean C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)OP…
S7P RCSB PDB A3N294 290.2 Da LogP -3.74 TPSA 177.1 1 viol. ✓ Clean C([C@H]([C@@H]1[C@H]([C@@H]([C@](O1)(CO)O)O)O)O…
TPS RCSB PDB P31550 345.3 Da LogP 0.72 TPSA 122.4 ✓ Ro5 ✓ Clean Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)O

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.

Cross-references

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