KpATCC43816 Protein target profile
bacterial extracellular solute-binding, 5 Middlefamily protein
Accession: VK055_4188
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.
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
- 0.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- N
- DEG identity (%)
- 29.082 Higher values support similarity to known essential genes.
Structure confidence
- ColabFold pLDDT
- 93.48 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.
MQAKTDSTSGHSLTLAIGEEPSEGFDPLLGWSHGSTLLLHSALLKQNVDMDWENFLTEHVEHSADGKIWTITLLPDLKFSDGSPLTAQDVAFTYNQAAQGGGKIDMGNFSAARVLDDRRVEITLSAPQSTFVSVLGSLGIVPQHQYDAKTYAQNPVGAGPYRLVSFQPGQQLIVEANPYYSGHRNDFDKLIFVFLDEDSAYAAAQSGQLGLVRVAPSVSVTPQQGLTLWVRPSVENRGIAFPTIPAGQKDANGYPIGNDVTADVAIRRAINYAIDRHLLANQLMEGHAVPAYSAVQGLPWDNPQAAFKDGDLATAKHILDDAGWEVGEDGIRVKNGKKAQLTLWYASGDSTRRDLAQAVSAMVKPLGIAMELKSGSWETVERHMHANPTLFGWGSLDPMELYHHYSSKAAGVEYYNPGYYSNNAVDQHLQQALNAPTWQQAVPVWQQVEWDGESGAGVRGDAAWAWLLNLQHTYLASPCIDLGNAAPEIHGSWSVLNNVQDWKWTCQ
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Subcellular localization
- Localization
- Periplasmic
Gene Ontology (GO)
3- GO:0043190 A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
- GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
- 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.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 1 | 496 | PIRSF | PIRSF002741 | MppA |
| 1 | 496 | InterPro | IPR030678 | Peptide/nickel binding protein, MppA-type |
| 14 | 480 | PANTHER | PTHR30290 | PERIPLASMIC BINDING COMPONENT OF ABC TRANSPORTER |
| 14 | 480 | InterPro | IPR039424 | Solute-binding protein family 5 |
| 56 | 407 | Pfam | PF00496 | Bacterial extracellular solute-binding proteins, family 5 Middle |
| 56 | 407 | InterPro | IPR000914 | Solute-binding protein family 5 domain |
| 25 | 231 | Gene3D | G3DSA:3.40.190.10 | - |
| 232 | 475 | Gene3D | G3DSA:3.10.105.10 | - |
| 232 | 474 | FunFam | G3DSA:3.10.105.10:FF:000009 | ABC transporter substrate-binding protein |
| 13 | 483 | CDD | cd08518 | PBP2_NikA_DppA_OppA_like_19 |
| 8 | 480 | SUPERFAMILY | SSF53850 | Periplasmic binding protein-like II |
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_A0ABD7NX05
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_4188
|
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 |
|---|---|---|---|---|---|---|
| 8UX RCSB PDB | Q2FVE7 | 328.3 Da LogP -1.10 TPSA 164.6 | 1 viol. | ✓ Clean |
C[C@@H](C(=O)O)N[C@@H](CCN[C@H](Cc1c[nH]cn1)C(=…
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| N72 RCSB PDB | O50271 | 309.3 Da LogP -3.46 TPSA 184.6 | 1 viol. | ✓ Clean |
C(CC(=O)O)[C@H](C(=O)O)NCC(=O)[C@@H]([C@@H]([C@…
|
|
| N7T RCSB PDB | O50271 | 309.3 Da LogP -3.46 TPSA 184.6 | 1 viol. | ✓ Clean |
C(CC(=O)O)[C@@H](C(=O)O)NCC(=O)[C@H]([C@@H]([C@…
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| NGE RCSB PDB | Q7VL18 | 325.3 Da LogP -4.90 TPSA 197.0 | 1 viol. | ✓ Clean |
C1[C@@H]([C@H]([C@@H](O[C@@]1(C(=O)O)O)[C@@H]([…
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| OXL RCSB PDB | Q0P844 | 88.0 Da LogP -3.51 TPSA 80.3 | ✓ Ro5 | ✓ Clean |
C(=O)(C(=O)[O-])[O-]
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| SLB RCSB PDB | Q7VL18 | 309.3 Da LogP -3.87 TPSA 176.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@@H]1[C@H](C[C@](O[C@H]1[C@@H]([C@@H](…
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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 |
|---|---|---|---|---|---|
| ZINC106403632 ZINC | 1.000 | 325.3 Da LogP -4.90 TPSA 197.0 | 1 viol. | ✓ Clean |
O=C(CO)N[C@H]1[C@@H]([C@H](O)[C@H](O)CO)O[C@@](…
|
| ZINC12359995 ZINC | 1.000 | 309.3 Da LogP -3.87 TPSA 176.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@@H]1[C@H](O)C[C@](O)(C(=O)O)O[C@H]1[C…
|
| ZINC15206143 ZINC | 1.000 | 309.3 Da LogP -3.87 TPSA 176.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@H]1[C@@H]([C@@H](O)[C@@H](O)CO)O[C@@]…
|
| ZINC15206146 ZINC | 1.000 | 309.3 Da LogP -3.87 TPSA 176.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@H]1[C@@H]([C@H](O)[C@@H](O)CO)O[C@@](…
|
| ZINC15206149 ZINC | 1.000 | 309.3 Da LogP -3.87 TPSA 176.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@@H]1[C@H](O)C[C@](O)(C(=O)O)O[C@H]1[C…
|
| ZINC1532591 ZINC | 1.000 | 309.3 Da LogP -3.87 TPSA 176.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@@H]1[C@@H]([C@H](O)[C@H](O)CO)O[C@@](…
|
| ZINC247362640 ZINC | 1.000 | 325.3 Da LogP -4.90 TPSA 197.0 | 1 viol. | ✓ Clean |
O=C(CO)N[C@H]1[C@@H]([C@H](O)[C@@H](O)CO)O[C@@]…
|
| ZINC247362642 ZINC | 1.000 | 325.3 Da LogP -4.90 TPSA 197.0 | 1 viol. | ✓ Clean |
O=C(CO)N[C@H]1[C@@H]([C@@H](O)[C@@H](O)CO)O[C@@…
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| ZINC247362655 ZINC | 1.000 | 325.3 Da LogP -4.90 TPSA 197.0 | 1 viol. | ✓ Clean |
O=C(CO)N[C@H]1[C@@H]([C@@H](O)[C@H](O)CO)O[C@@]…
|
| ZINC2586055 ZINC | 1.000 | 309.3 Da LogP -3.87 TPSA 176.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@H]1[C@@H](O)C[C@](O)(C(=O)O)O[C@@H]1[…
|
| ZINC3793840 ZINC | 1.000 | 309.3 Da LogP -3.87 TPSA 176.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@@H]1[C@@H](O)C[C@@](O)(C(=O)O)O[C@H]1…
|
| ZINC3870085 ZINC | 1.000 | 309.3 Da LogP -3.87 TPSA 176.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@H]1[C@@H]([C@H](O)[C@H](O)CO)O[C@@](O…
|
| ZINC3870086 ZINC | 1.000 | 309.3 Da LogP -3.87 TPSA 176.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@@H]1[C@@H](O)C[C@](O)(C(=O)O)O[C@@H]1…
|
| ZINC4081651 ZINC | 1.000 | 309.3 Da LogP -3.87 TPSA 176.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@@H]1[C@@H](O)C[C@](O)(C(=O)O)O[C@H]1[…
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| ZINC4096097 ZINC | 1.000 | 325.3 Da LogP -4.90 TPSA 197.0 | 1 viol. | ✓ Clean |
O=C(CO)N[C@@H]1[C@@H](O)C[C@@](O)(C(=O)O)O[C@H]…
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| ZINC4293691 ZINC | 1.000 | 309.3 Da LogP -3.87 TPSA 176.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@@H]1[C@@H](O)C[C@@](O)(C(=O)O)O[C@@H]…
|
| ZINC43509538 ZINC | 1.000 | 309.3 Da LogP -3.87 TPSA 176.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@H]1[C@@H](O)C[C@@](O)(C(=O)O)O[C@H]1[…
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| ZINC44790306 ZINC | 1.000 | 309.3 Da LogP -3.87 TPSA 176.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@@H]1[C@@H](O)C[C@](O)(C(=O)O)O[C@@H]1…
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| ZINC5227885 ZINC | 1.000 | 309.3 Da LogP -3.87 TPSA 176.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@@H]1[C@H](O)C[C@](O)(C(=O)O)O[C@H]1[C…
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| ZINC71789682 ZINC | 1.000 | 309.3 Da LogP -3.87 TPSA 176.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@@H]1[C@@H](O)C[C@](O)(C(=O)O)O[C@@H]1…
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| ZINC71789683 ZINC | 1.000 | 309.3 Da LogP -3.87 TPSA 176.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@@H]1[C@@H](O)C[C@](O)(C(=O)O)O[C@@H]1…
|
| ZINC71789800 ZINC | 1.000 | 309.3 Da LogP -3.87 TPSA 176.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@H]1[C@@H]([C@@H](O)[C@H](O)CO)O[C@@](…
|
| ZINC71789801 ZINC | 1.000 | 309.3 Da LogP -3.87 TPSA 176.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@@H]1[C@H](O)C[C@](O)(C(=O)O)O[C@H]1[C…
|
| ZINC79036671 ZINC | 1.000 | 309.3 Da LogP -3.46 TPSA 184.6 | 1 viol. | ✓ Clean |
O=C(O)CC[C@H](NCC(=O)[C@@H](O)[C@H](O)[C@H](O)C…
|
| ZINC33977700 ZINC | 0.818 | 308.3 Da LogP -3.91 TPSA 182.6 | 1 viol. | ✓ Clean |
CC(=O)N[C@@H]1[C@@H](O)C[C@@](O)(C(=O)O)O[C@H]1…
|
| ZINC100655903 ZINC | 0.783 | 323.3 Da LogP -3.78 TPSA 165.8 | 1 viol. | ✓ Clean |
COC(=O)[C@]1(O)C[C@H](O)[C@H](NC(C)=O)[C@H]([C@…
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| ZINC100655904 ZINC | 0.783 | 323.3 Da LogP -3.78 TPSA 165.8 | 1 viol. | ✓ Clean |
COC(=O)[C@]1(O)C[C@H](O)[C@H](NC(C)=O)[C@H]([C@…
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| ZINC100655906 ZINC | 0.783 | 323.3 Da LogP -3.78 TPSA 165.8 | 1 viol. | ✓ Clean |
COC(=O)[C@]1(O)C[C@H](O)[C@H](NC(C)=O)[C@H]([C@…
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| ZINC146216515 ZINC | 0.783 | 323.3 Da LogP -3.78 TPSA 165.8 | 1 viol. | ✓ Clean |
COC(=O)[C@@]1(O)C[C@@H](O)[C@@H](NC(C)=O)[C@H](…
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| ZINC2382416875 ZINC | 0.783 | 323.3 Da LogP -3.78 TPSA 165.8 | 1 viol. | ✓ Clean |
COC(=O)[C@@]1(O)C[C@H](O)[C@@H](NC(C)=O)[C@H]([…
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| ZINC2558706 ZINC | 0.783 | 323.3 Da LogP -3.78 TPSA 165.8 | 1 viol. | ✓ Clean |
COC(=O)[C@@]1(O)C[C@@H](O)[C@H](NC(C)=O)[C@@H](…
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| ZINC2586056 ZINC | 0.783 | 323.3 Da LogP -3.78 TPSA 165.8 | 1 viol. | ✓ Clean |
COC(=O)[C@@]1(O)C[C@H](O)[C@H](NC(C)=O)[C@@H]([…
|
| ZINC26254851 ZINC | 0.783 | 323.3 Da LogP -3.78 TPSA 165.8 | 1 viol. | ✓ Clean |
COC(=O)[C@@]1(O)C[C@H](O)[C@@H](NC(C)=O)[C@H]([…
|
| ZINC4293695 ZINC | 0.783 | 323.3 Da LogP -3.78 TPSA 165.8 | 1 viol. | ✓ Clean |
COC(=O)[C@]1(O)C[C@@H](O)[C@@H](NC(C)=O)[C@@H](…
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| ZINC4293696 ZINC | 0.783 | 323.3 Da LogP -3.78 TPSA 165.8 | 1 viol. | ✓ Clean |
COC(=O)[C@]1(O)C[C@H](O)[C@@H](NC(C)=O)[C@@H]([…
|
| ZINC4293697 ZINC | 0.783 | 323.3 Da LogP -3.78 TPSA 165.8 | 1 viol. | ✓ Clean |
COC(=O)[C@]1(O)C[C@@H](O)[C@@H](NC(C)=O)[C@H]([…
|
| ZINC4293698 ZINC | 0.783 | 323.3 Da LogP -3.78 TPSA 165.8 | 1 viol. | ✓ Clean |
COC(=O)[C@]1(O)C[C@H](O)[C@@H](NC(C)=O)[C@H]([C…
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| ZINC43771922 ZINC | 0.783 | 323.3 Da LogP -3.78 TPSA 165.8 | 1 viol. | ✓ Clean |
COC(=O)[C@]1(O)C[C@H](O)[C@@H](NC(C)=O)[C@H]([C…
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| ZINC4533821 ZINC | 0.783 | 323.3 Da LogP -3.78 TPSA 165.8 | 1 viol. | ✓ Clean |
COC(=O)[C@@]1(O)C[C@@H](O)[C@@H](NC(C)=O)[C@@H]…
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| ZINC4533822 ZINC | 0.783 | 323.3 Da LogP -3.78 TPSA 165.8 | 1 viol. | ✓ Clean |
COC(=O)[C@@]1(O)C[C@H](O)[C@@H](NC(C)=O)[C@@H](…
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| ZINC64220345 ZINC | 0.783 | 323.3 Da LogP -3.78 TPSA 165.8 | 1 viol. | ✓ Clean |
COC(=O)[C@]1(O)C[C@H](O)[C@H](NC(C)=O)[C@H]([C@…
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| ZINC76938880 ZINC | 0.783 | 323.3 Da LogP -3.78 TPSA 165.8 | 1 viol. | ✓ Clean |
COC(=O)[C@]1(O)C[C@@H](O)[C@@H](NC(C)=O)[C@H]([…
|
| ZINC95635434 ZINC | 0.783 | 323.3 Da LogP -3.78 TPSA 165.8 | 1 viol. | ✓ Clean |
COC(=O)[C@@]1(O)C[C@@H](O)[C@@H](NC(C)=O)[C@H](…
|
| ZINC4096286 ZINC | 0.750 | 351.3 Da LogP -3.30 TPSA 182.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@@H]1[C@@H](O)C[C@@](O)(C(=O)O)O[C@H]1…
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| ZINC96327832 ZINC | 0.750 | 351.3 Da LogP -3.30 TPSA 182.8 | 1 viol. | ✓ Clean |
CC(=O)N[C@@H]1[C@@H](O)C[C@](O)(C(=O)O)O[C@H]1[…
|
| ZINC16123778 ZINC | 0.694 | 323.3 Da LogP -3.22 TPSA 165.8 | 1 viol. | ✓ Clean |
CO[C@]1(C(=O)O)C[C@@H](O)[C@@H](NC(C)=O)[C@H]([…
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| ZINC247941808 ZINC | 0.694 | 323.3 Da LogP -3.22 TPSA 165.8 | 1 viol. | ✓ Clean |
CO[C@]1(C(=O)O)C[C@H](O)[C@H](NC(C)=O)[C@H]([C@…
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| ZINC4557072 ZINC | 0.694 | 323.3 Da LogP -3.22 TPSA 165.8 | 1 viol. | ✓ Clean |
CO[C@]1(C(=O)O)C[C@H](O)[C@@H](NC(C)=O)[C@@H]([…
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| ZINC5884114 ZINC | 0.694 | 323.3 Da LogP -3.22 TPSA 165.8 | 1 viol. | ✓ Clean |
CO[C@]1(C(=O)O)C[C@H](O)[C@@H](NC(C)=O)[C@H]([C…
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| ZINC76935790 ZINC | 0.694 | 323.3 Da LogP -3.22 TPSA 165.8 | 1 viol. | ✓ Clean |
CO[C@]1(C(=O)O)C[C@H](O)[C@H](NC(C)=O)[C@H]([C@…
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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.