KpATCC43816 Protein target profile
bacterial extracellular solute-binding family protein
Accession: VK055_0597
Promising target candidate with multiple supporting evidence streams.
Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.
Main supporting evidence
Risks to review
Evidence coverage
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)
- Y
- DEG identity (%)
- 41.993 Higher values support similarity to known essential genes.
- DEG E-value
- 3.83e-75 Smaller values mean stronger essential-gene similarity.
Structure confidence
- ColabFold pLDDT
- 90.84 0-100 confidence; >70 supports local structural interpretation.
Binding-site evidence
AlphaFold DB / UniProt modelP2Rank'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.
Sequence
Primary amino-acid sequence viewer.
MNTVMTVKKGVVLAMALSAMMLSSAHALTVYTAGPGSLAKSLASGFEQQTGVKVTVFQATTGKVMARLEAEQANPQADVLISASWDTAEDLHQRGWLLPFASANADQVPANLKSADYIAQGVSALGIVWNSKSGTPEPKEWRDLTQPAFKDKVTTPDPALSGASLDLLIGLQNSMGDQAWQLFDDLKKNGMVVSGPNAQAVTPVMQGAKAAVFGAVDYVSYGNIQQGESLKVIFPASGTVIAPRPMMILKTSQHADDAKAFIDYVLSPEGQAKVADAWLMPARRDVAAKRPLLDALKVLPTTSEGSSERGAVLARFSQLYAQ
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Subcellular localization
- Localization
- Periplasmic
Gene Ontology (GO)
5- 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:0046872 Binding to a metal ion.
- 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.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 1 | 27 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM |
| 1 | 10 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. |
| 12 | 34 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. |
| 25 | 295 | SUPERFAMILY | SSF53850 | Periplasmic binding protein-like II |
| 12 | 292 | PANTHER | PTHR30006 | THIAMINE-BINDING PERIPLASMIC PROTEIN-RELATED |
| 1 | 27 | Phobius | SIGNAL_PEPTIDE | Signal peptide region |
| 1 | 27 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM |
| 23 | 27 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. |
| 28 | 322 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. |
| 3 | 310 | PIRSF | PIRSF002825 | CfbpA |
| 3 | 310 | InterPro | IPR026045 | Ferric binding protein |
| 11 | 22 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. |
| 126 | 296 | Gene3D | G3DSA:3.40.190.10 | - |
| 74 | 296 | Pfam | PF13343 | Bacterial extracellular solute-binding protein |
| 28 | 281 | CDD | cd13547 | PBP2_Fbp_like_2 |
| 29 | 292 | Gene3D | G3DSA:3.40.190.10 | - |
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.
How colors and pocket overlays are used
Pocket details Inspect a specific pocket, or open the full viewer
- Method
- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
Selecting a pocket opens its details and centers the viewer without clearing other active layers. Use Focus this pocket when you want to hide the rest; use Surface for the wider residue environment.
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Residue sets
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Residue sets
All structural evidence
Structural evidence
0 + 2Experimental 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_A0A0H3GNX4
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_0597
|
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.
Structural ligand evidence is available for this target.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.
No PDB structure with a co-crystallized ligand found for this exact protein.
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.
| Ligand | Source crystal | UniProt (homolog) | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| EDT RCSB PDB | P35755 | 292.2 Da LogP -2.07 TPSA 155.7 | ✓ Ro5 | ✓ Clean |
C(CN(CC(=O)O)CC(=O)O)N(CC(=O)O)CC(=O)O
|
|
| 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)(…
|
|
| FLC RCSB PDB | Q10Z45 | 189.1 Da LogP -5.25 TPSA 140.6 | ✓ Ro5 | ✓ Clean |
C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])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…
|
|
| MLA RCSB PDB | X5DVD1 | 104.1 Da LogP -0.45 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
C(C(=O)O)C(=O)O
|
|
| 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…
|
Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL bioactivity data found for this exact protein.
Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL hits found through similar proteins.
Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).
| Ligand | Tanimoto | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|
| ZINC100351935 ZINC | 1.000 | 260.1 Da LogP -3.10 TPSA 156.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@…
|
| ZINC1529564 ZINC | 1.000 | 260.1 Da LogP -3.10 TPSA 156.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@@H]1O[C@@H](O)[C@H](O)[C@H](O)[C@…
|
| ZINC1532533 ZINC | 1.000 | 260.1 Da LogP -3.10 TPSA 156.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@@H]1O[C@H](O)[C@@H](O)[C@H](O)[C@…
|
| ZINC1532857 ZINC | 1.000 | 260.1 Da LogP -3.10 TPSA 156.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C…
|
| ZINC3581460 ZINC | 1.000 | 260.1 Da LogP -3.10 TPSA 156.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C…
|
| ZINC38276879 ZINC | 1.000 | 260.1 Da LogP -3.10 TPSA 156.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C@…
|
| ZINC38276880 ZINC | 1.000 | 260.1 Da LogP -3.10 TPSA 156.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@H](O)[C@@H](O)[C@H](O)[C@H…
|
| ZINC3869397 ZINC | 1.000 | 260.1 Da LogP -3.10 TPSA 156.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C…
|
| ZINC3875374 ZINC | 1.000 | 260.1 Da LogP -3.10 TPSA 156.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C@…
|
| ZINC3875375 ZINC | 1.000 | 260.1 Da LogP -3.10 TPSA 156.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@…
|
| ZINC4095545 ZINC | 1.000 | 260.1 Da LogP -3.10 TPSA 156.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C@…
|
| ZINC4095546 ZINC | 1.000 | 260.1 Da LogP -3.10 TPSA 156.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@H…
|
| ZINC4096188 ZINC | 1.000 | 260.1 Da LogP -3.10 TPSA 156.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@H](O)[C@@H](O)[C@@H](O)[C@…
|
| ZINC4096690 ZINC | 1.000 | 260.1 Da LogP -3.10 TPSA 156.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@](O)(CO)[C@@H](O)[C@@H]1O
|
| ZINC8551507 ZINC | 1.000 | 260.1 Da LogP -3.10 TPSA 156.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@@H]1O[C@H](O)[C@@H](O)[C@H](O)[C@…
|
| ZINC12504154 ZINC | 0.962 | 230.1 Da LogP -2.47 TPSA 136.7 | ✓ Ro5 | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@H](O)[C@@H](O)[C@@H]1O
|
| ZINC1532546 ZINC | 0.962 | 230.1 Da LogP -2.47 TPSA 136.7 | ✓ Ro5 | ✓ Clean |
O=P(O)(O)OC[C@@H]1O[C@H](O)[C@@H](O)[C@H]1O
|
| ZINC4096190 ZINC | 0.962 | 230.1 Da LogP -2.47 TPSA 136.7 | ✓ Ro5 | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@H](O)[C@H](O)[C@@H]1O
|
| ZINC4228241 ZINC | 0.962 | 230.1 Da LogP -2.47 TPSA 136.7 | ✓ Ro5 | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O
|
| ZINC4521831 ZINC | 0.962 | 230.1 Da LogP -2.47 TPSA 136.7 | ✓ Ro5 | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@@H](O)[C@@H](O)[C@@H]1O
|
| ZINC19364891 ZINC | 0.737 | 204.2 Da LogP -0.98 TPSA 81.1 | ✓ Ro5 | ✓ Clean |
CN(C)CCN(CC(=O)O)CC(=O)O
|
| ZINC19364892 ZINC | 0.737 | 232.3 Da LogP -0.20 TPSA 81.1 | ✓ Ro5 | ✓ Clean |
CCN(CC)CCN(CC(=O)O)CC(=O)O
|
| ZINC19366122 ZINC | 0.737 | 278.3 Da LogP -2.16 TPSA 138.6 | ✓ Ro5 | ✓ Clean |
O=C(O)CN(CCO)CCN(CC(=O)O)CC(=O)O
|
| ZINC5908834 ZINC | 0.737 | 379.3 Da LogP -2.09 TPSA 196.2 | ✓ Ro5 | ✓ Clean |
O=C(O)CN(CCN(CCN(CC(=O)O)CC(=O)O)C(=O)O)CC(=O)O
|
| ZINC13516910 ZINC | 0.733 | 244.1 Da LogP -2.42 TPSA 136.7 | ✓ Ro5 | ✓ Clean |
O=P(O)(O)OC[C@@H]1O[C@@H](CO)[C@@H](O)[C@H]1O
|
| ZINC2562340 ZINC | 0.733 | 244.1 Da LogP -2.42 TPSA 136.7 | ✓ Ro5 | ✓ Clean |
O=P(O)(O)OC[C@@H]1O[C@@H](CO)[C@H](O)[C@H]1O
|
| ZINC4097102 ZINC | 0.719 | 259.2 Da LogP -3.14 TPSA 162.7 | 1 viol. | ✓ Clean |
N[C@H]1[C@H](O)O[C@H](COP(=O)(O)O)[C@@H](O)[C@@…
|
| ZINC4097103 ZINC | 0.719 | 259.2 Da LogP -3.14 TPSA 162.7 | 1 viol. | ✓ Clean |
N[C@H]1[C@@H](O)O[C@H](COP(=O)(O)O)[C@@H](O)[C@…
|
| ZINC149813449 ZINC | 0.700 | 278.2 Da LogP -1.48 TPSA 155.7 | ✓ Ro5 | ✓ Clean |
O=C(O)CN(CCN(CC(=O)O)C(=O)O)CC(=O)O
|
| ZINC1532902 ZINC | 0.700 | 206.2 Da LogP -0.86 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O
|
| ZINC2018106 ZINC | 0.700 | 206.2 Da LogP -0.86 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
O=C(O)CC[C@](O)(CC(=O)O)C(=O)O
|
| ZINC12502703 ZINC | 0.667 | 340.1 Da LogP -2.99 TPSA 203.4 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@@H](OP(=O)(O)O)[C@H](O)[C@…
|
| ZINC4095589 ZINC | 0.667 | 340.1 Da LogP -2.99 TPSA 203.4 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@H](OP(=O)(O)O)[C@H](O)[C@@…
|
| ZINC90669676 ZINC | 0.667 | 377.4 Da LogP -2.57 TPSA 176.0 | ✓ Ro5 | ✓ Clean |
O=CCN(CCN(CC(=O)O)CC(=O)O)CCN(CC(=O)O)CC(=O)O
|
| ZINC15298193 ZINC | 0.657 | 422.3 Da LogP -5.28 TPSA 236.1 | 2 viol. | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@@H…
|
| ZINC1933262384 ZINC | 0.657 | 422.3 Da LogP -5.28 TPSA 236.1 | 2 viol. | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@@H…
|
| ZINC1933262385 ZINC | 0.657 | 422.3 Da LogP -5.28 TPSA 236.1 | 2 viol. | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@@H…
|
| ZINC1933262386 ZINC | 0.657 | 422.3 Da LogP -5.28 TPSA 236.1 | 2 viol. | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@H]…
|
| ZINC1933262387 ZINC | 0.657 | 422.3 Da LogP -5.28 TPSA 236.1 | 2 viol. | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@H]…
|
| ZINC256073272 ZINC | 0.657 | 422.3 Da LogP -5.28 TPSA 236.1 | 2 viol. | ✓ Clean |
O=P(O)(O)OC[C@@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@H…
|
| ZINC256073273 ZINC | 0.657 | 422.3 Da LogP -5.28 TPSA 236.1 | 2 viol. | ✓ Clean |
O=P(O)(O)OC[C@@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@@…
|
| ZINC256073274 ZINC | 0.657 | 422.3 Da LogP -5.28 TPSA 236.1 | 2 viol. | ✓ Clean |
O=P(O)(O)OC[C@@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@H…
|
| ZINC256073275 ZINC | 0.657 | 422.3 Da LogP -5.28 TPSA 236.1 | 2 viol. | ✓ Clean |
O=P(O)(O)OC[C@@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@@…
|
| ZINC4228300 ZINC | 0.657 | 422.3 Da LogP -5.28 TPSA 236.1 | 2 viol. | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@H](O[C@H]2O[C@H](CO)[C@@H]…
|
| ZINC56870785 ZINC | 0.656 | 228.1 Da LogP -1.40 TPSA 116.5 | ✓ Ro5 | ✓ Clean |
C[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](O)[C@H]1O
|
| ZINC3593496 ZINC | 0.652 | 206.2 Da LogP -1.16 TPSA 121.1 | ✓ Ro5 | ✓ Clean |
COC(=O)C[C@@](O)(CC(=O)O)C(=O)O
|
| ZINC3593497 ZINC | 0.652 | 206.2 Da LogP -1.16 TPSA 121.1 | ✓ Ro5 | ✓ Clean |
COC(=O)C[C@](O)(CC(=O)O)C(=O)O
|
| ZINC22052182 ZINC | 0.650 | 336.3 Da LogP -2.05 TPSA 164.9 | ✓ Ro5 | ✓ Clean |
O=C(O)CN(CCOCCN(CC(=O)O)CC(=O)O)CC(=O)O
|
| ZINC13522068 ZINC | 0.636 | 310.1 Da LogP -2.35 TPSA 183.2 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@H]1O[C@H](OP(=O)(O)O)[C@H](O)[C@@…
|
| ZINC217755395 ZINC | 0.636 | 263.2 Da LogP -1.47 TPSA 147.8 | ✓ Ro5 | ✓ Clean |
O=NN(CCN(CC(=O)O)CC(=O)O)CC(=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.