KpATCC43816 Protein target profile
ABC sugar (Ribose) transporter, periplasmic substrate-binding subunit
Accession: VK055_1892
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
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
- 0.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- N
- DEG identity (%)
- 26.846 Higher values support similarity to known essential genes.
Structure confidence
- ColabFold pLDDT
- 93.19 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.
MSQKRKLLPAALGLLSLASLSVAAADALSLQGKTIGVAVVGTQHFWDREAFKGATEEVEKLGGKVIGVDGGRDNQVHANNHDILLSRKVDAVISILGDSAVEPKFKALRDAGIPVFTVDHVSQYSVNNTTSDNYTLGSTIGRYMADELGGKGNVAVFNAFSSALRICGIRYDQWKYVLKDYPDIHIIQPELAEQFANSPEDARKKTLELLSQYPKGKLDAIHVACWDQPAIGIVQALEETGRDKDVKVTAIDAGPETLEIMAEPGSPFVANVAQQPHLIGQTSADNVARYFAGQKLPVQTFIPVVPVKGPQEAKAVYKQLGYGELQ
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Subcellular localization
- Localization
- Periplasmic
Gene Ontology (GO)
3- GO:0030313 An envelope that surrounds a bacterial cell and includes the cytoplasmic membrane and everything external, encompassing the periplasmic space, cell wall, and outer membrane if present.
- GO:0030246 Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
- GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 15 | 305 | PANTHER | PTHR46847 | D-ALLOSE-BINDING PERIPLASMIC PROTEIN-RELATED |
| 1 | 23 | Phobius | SIGNAL_PEPTIDE | Signal peptide region |
| 24 | 326 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. |
| 1 | 25 | SignalP_EUK | SignalP-noTM | SignalP-noTM |
| 35 | 295 | Pfam | PF13407 | Periplasmic binding protein domain |
| 35 | 295 | InterPro | IPR025997 | Periplasmic binding protein |
| 34 | 307 | CDD | cd06305 | PBP1_methylthioribose_binding-like |
| 19 | 23 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. |
| 132 | 277 | Gene3D | G3DSA:3.40.50.2300 | - |
| 1 | 6 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. |
| 54 | 299 | Gene3D | G3DSA:3.40.50.2300 | - |
| 1 | 24 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM |
| 7 | 18 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. |
| 1 | 27 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM |
| 7 | 29 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. |
| 32 | 307 | SUPERFAMILY | SSF53822 | Periplasmic binding protein-like I |
| 32 | 307 | InterPro | IPR028082 | Periplasmic binding protein-like I |
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
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
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_A0A0H3GPU0
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_1892
|
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 |
|---|---|---|---|---|---|---|
| 3VB RCSB PDB | A0QYB5 | 122.1 Da LogP -2.31 TPSA 80.9 | ✓ Ro5 | ✓ Clean |
C([C@H]([C@@H](CO)O)O)O
|
|
| 62W RCSB PDB | A0QYB3 | 182.2 Da LogP -3.59 TPSA 121.4 | 1 viol. | ✓ Clean |
C([C@H]([C@@H]([C@H]([C@H](CO)O)O)O)O)O
|
|
| GZL RCSB PDB | P39325 | 180.2 Da LogP -3.22 TPSA 110.4 | ✓ Ro5 | ✓ Clean |
C(C([C@H]1C(C([C@@H](O1)O)O)O)O)O
|
|
| RIP RCSB PDB | Q8E283 | 150.1 Da LogP -2.58 TPSA 90.2 | ✓ Ro5 | ✓ Clean |
C1[C@H]([C@H]([C@H]([C@@H](O1)O)O)O)O
|
|
| X9X RCSB PDB | B9K0E0 | 182.2 Da LogP -3.59 TPSA 121.4 | 1 viol. | ✓ Clean |
C([C@H]([C@H]([C@H]([C@H](CO)O)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 |
|---|---|---|---|---|---|
| ZINC15657695 ZINC | 0.955 | 210.2 Da LogP -3.86 TPSA 130.6 | 1 viol. | ✓ Clean |
OC[C@@H](O)[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@…
|
| ZINC25721048 ZINC | 0.955 | 210.2 Da LogP -3.86 TPSA 130.6 | 1 viol. | ✓ Clean |
OC[C@@H](O)[C@@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C…
|
| ZINC25721054 ZINC | 0.955 | 210.2 Da LogP -3.86 TPSA 130.6 | 1 viol. | ✓ Clean |
OC[C@@H](O)[C@@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@…
|
| ZINC4726901 ZINC | 0.955 | 210.2 Da LogP -3.86 TPSA 130.6 | 1 viol. | ✓ Clean |
OC[C@H](O)[C@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C@…
|
| ZINC4726902 ZINC | 0.955 | 210.2 Da LogP -3.86 TPSA 130.6 | 1 viol. | ✓ Clean |
OC[C@@H](O)[C@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C…
|
| ZINC4726903 ZINC | 0.955 | 210.2 Da LogP -3.86 TPSA 130.6 | 1 viol. | ✓ Clean |
OC[C@H](O)[C@@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C…
|
| ZINC4726904 ZINC | 0.955 | 210.2 Da LogP -3.86 TPSA 130.6 | 1 viol. | ✓ Clean |
OC[C@@H](O)[C@@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[…
|
| ZINC100055463 ZINC | 0.917 | 212.2 Da LogP -4.22 TPSA 141.6 | 1 viol. | ✓ Clean |
OC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)CO
|
| ZINC100064885 ZINC | 0.917 | 212.2 Da LogP -4.22 TPSA 141.6 | 1 viol. | ✓ Clean |
OC[C@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO
|
| ZINC17780060 ZINC | 0.917 | 212.2 Da LogP -4.22 TPSA 141.6 | 1 viol. | ✓ Clean |
OC[C@@H](O)[C@H](O)C(O)[C@H](O)[C@H](O)CO
|
| ZINC17952732 ZINC | 0.917 | 212.2 Da LogP -4.22 TPSA 141.6 | 1 viol. | ✓ Clean |
OC[C@H](O)[C@@H](O)C(O)[C@H](O)[C@H](O)CO
|
| ZINC18042331 ZINC | 0.917 | 242.2 Da LogP -4.86 TPSA 161.8 | 1 viol. | ✓ Clean |
OC[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H]…
|
| ZINC18120313 ZINC | 0.917 | 212.2 Da LogP -4.22 TPSA 141.6 | 1 viol. | ✓ Clean |
OC[C@H](O)[C@H](O)C(O)[C@H](O)[C@H](O)CO
|
| ZINC3979006 ZINC | 0.917 | 212.2 Da LogP -4.22 TPSA 141.6 | 1 viol. | ✓ Clean |
OC[C@@H](O)[C@@H](O)C(O)[C@H](O)[C@H](O)CO
|
| ZINC4403103 ZINC | 0.917 | 242.2 Da LogP -4.86 TPSA 161.8 | 1 viol. | ✓ Clean |
OC[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H…
|
| ZINC4403105 ZINC | 0.917 | 242.2 Da LogP -4.86 TPSA 161.8 | 1 viol. | ✓ Clean |
OC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H…
|
| ZINC4403107 ZINC | 0.917 | 242.2 Da LogP -4.86 TPSA 161.8 | 1 viol. | ✓ Clean |
OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@…
|
| ZINC9212412 ZINC | 0.917 | 212.2 Da LogP -4.22 TPSA 141.6 | 1 viol. | ✓ Clean |
OC[C@H](O)[C@@H](O)C(O)[C@H](O)[C@@H](O)CO
|
| ZINC5201837 ZINC | 0.647 | 345.3 Da LogP -6.55 TPSA 214.3 | 2 viol. | ✓ Clean |
OC[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CNC[C@H](…
|
| ZINC5201838 ZINC | 0.647 | 345.3 Da LogP -6.55 TPSA 214.3 | 2 viol. | ✓ Clean |
OC[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CNC[C@@H]…
|
| ZINC5201839 ZINC | 0.647 | 345.3 Da LogP -6.55 TPSA 214.3 | 2 viol. | ✓ Clean |
OC[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CNC[C@H](…
|
| ZINC5201841 ZINC | 0.647 | 345.3 Da LogP -6.55 TPSA 214.3 | 2 viol. | ✓ Clean |
OC[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CNC[C@@H]…
|
| ZINC101356848 ZINC | 0.579 | 388.4 Da LogP -6.96 TPSA 226.4 | 2 viol. | ✓ Clean |
OC[C@H](O)[C@H](O)[C@H](O)[C@H](O)CNCCNC[C@H](O…
|
| ZINC215968865 ZINC | 0.579 | 388.4 Da LogP -6.96 TPSA 226.4 | 2 viol. | ✓ Clean |
OC[C@H](O)[C@H](O)[C@H](O)[C@H](O)CNCCNC[C@H](O…
|
| ZINC215968917 ZINC | 0.579 | 388.4 Da LogP -6.96 TPSA 226.4 | 2 viol. | ✓ Clean |
OC[C@H](O)[C@H](O)[C@H](O)[C@H](O)CNCCNC[C@H](O…
|
| ZINC215968963 ZINC | 0.579 | 388.4 Da LogP -6.96 TPSA 226.4 | 2 viol. | ✓ Clean |
OC[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CNCCNC[C@@H…
|
| ZINC216185927 ZINC | 0.579 | 209.2 Da LogP -3.02 TPSA 104.4 | ✓ Ro5 | ✓ Clean |
CN(C)C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)CO
|
| ZINC216185976 ZINC | 0.579 | 209.2 Da LogP -3.02 TPSA 104.4 | ✓ Ro5 | ✓ Clean |
CN(C)C[C@H](O)[C@H](O)[C@@H](O)[C@H](O)CO
|
| ZINC216186168 ZINC | 0.579 | 224.3 Da LogP -2.87 TPSA 101.2 | ✓ Ro5 | ✓ Clean |
C[N+](C)(C)C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)CO
|
| ZINC216186206 ZINC | 0.579 | 224.3 Da LogP -2.87 TPSA 101.2 | ✓ Ro5 | ✓ Clean |
C[N+](C)(C)C[C@H](O)[C@H](O)[C@@H](O)[C@H](O)CO
|
| ZINC25624721 ZINC | 0.579 | 209.2 Da LogP -3.02 TPSA 104.4 | ✓ Ro5 | ✓ Clean |
CN(C)C[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO
|
| ZINC25624980 ZINC | 0.579 | 224.3 Da LogP -2.87 TPSA 101.2 | ✓ Ro5 | ✓ Clean |
C[N+](C)(C)C[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO
|
| ZINC4566610 ZINC | 0.579 | 209.2 Da LogP -3.02 TPSA 104.4 | ✓ Ro5 | ✓ Clean |
CN(C)C[C@H](O)[C@H](O)[C@H](O)[C@H](O)CO
|
| ZINC4566614 ZINC | 0.579 | 224.3 Da LogP -2.87 TPSA 101.2 | ✓ Ro5 | ✓ Clean |
C[N+](C)(C)C[C@H](O)[C@H](O)[C@H](O)[C@H](O)CO
|
| ZINC255980408 ZINC | 0.577 | 414.4 Da LogP -5.66 TPSA 208.0 | 2 viol. | ✓ Clean |
O[C@H]1OC[C@@H](O[C@H]2OC[C@@H](O[C@H]3OC[C@@H]…
|
| ZINC255980409 ZINC | 0.577 | 414.4 Da LogP -5.66 TPSA 208.0 | 2 viol. | ✓ Clean |
O[C@H]1OC[C@@H](O[C@H]2OC[C@@H](O[C@H]3OC[C@@H]…
|
| ZINC255980410 ZINC | 0.577 | 414.4 Da LogP -5.66 TPSA 208.0 | 2 viol. | ✓ Clean |
O[C@@H]1[C@H](O)[C@@H](O[C@@H]2CO[C@H](O[C@@H]3…
|
| ZINC255980411 ZINC | 0.577 | 414.4 Da LogP -5.66 TPSA 208.0 | 2 viol. | ✓ Clean |
O[C@H]1OC[C@@H](O[C@H]2OC[C@@H](O[C@H]3OC[C@@H]…
|
| ZINC263584059 ZINC | 0.577 | 414.4 Da LogP -5.66 TPSA 208.0 | 2 viol. | ✓ Clean |
O[C@@H]1[C@@H](O[C@@H]2OC[C@@H](O)[C@H](O)[C@H]…
|
| ZINC263584060 ZINC | 0.577 | 414.4 Da LogP -5.66 TPSA 208.0 | 2 viol. | ✓ Clean |
O[C@H]1[C@H](O)[C@@H](O[C@@H]2CO[C@@H](O)[C@H](…
|
| ZINC263584061 ZINC | 0.577 | 414.4 Da LogP -5.66 TPSA 208.0 | 2 viol. | ✓ Clean |
O[C@@H]1[C@@H](O[C@H]2OC[C@@H](O)[C@H](O)[C@H]2…
|
| ZINC4095690 ZINC | 0.577 | 282.2 Da LogP -4.12 TPSA 149.1 | 1 viol. | ✓ Clean |
O[C@H]1[C@H](O)CO[C@@H](O[C@@H]2CO[C@H](O)[C@H]…
|
| ZINC4095691 ZINC | 0.577 | 282.2 Da LogP -4.12 TPSA 149.1 | 1 viol. | ✓ Clean |
O[C@H]1[C@H](O)CO[C@@H](O[C@@H]2CO[C@@H](O)[C@H…
|
| ZINC64622127 ZINC | 0.577 | 414.4 Da LogP -5.66 TPSA 208.0 | 2 viol. | ✓ Clean |
O[C@H]1[C@H](O)CO[C@@H](O[C@@H]2CO[C@@H](O[C@@H…
|
| ZINC78590548 ZINC | 0.577 | 414.4 Da LogP -5.66 TPSA 208.0 | 2 viol. | ✓ Clean |
O[C@H]1[C@H](O)CO[C@@H](O[C@@H]2CO[C@@H](O[C@@H…
|
| ZINC85546060 ZINC | 0.577 | 414.4 Da LogP -5.66 TPSA 208.0 | 2 viol. | ✓ Clean |
O[C@H]1[C@H](O)[C@@H](O[C@@H]2CO[C@@H](O)[C@H](…
|
| ZINC12953159 ZINC | 0.550 | 210.2 Da LogP -4.02 TPSA 138.5 | 1 viol. | ✓ Clean |
O=C[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@@H](O)CO
|
| ZINC12953168 ZINC | 0.550 | 210.2 Da LogP -4.02 TPSA 138.5 | 1 viol. | ✓ Clean |
O=C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO
|
| ZINC4353167 ZINC | 0.550 | 240.2 Da LogP -4.66 TPSA 158.7 | 1 viol. | ✓ Clean |
O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O…
|
| ZINC5830322 ZINC | 0.550 | 226.2 Da LogP -4.13 TPSA 158.7 | 1 viol. | ✓ Clean |
O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@@H](O)[C@H](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.