KpATCC43816 Protein target profile

bacterial extracellular solute-binding, 5 Middlefamily protein

Accession: VK055_0456

Gene: AIK79082.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GQV3
Length 567
Pocket druggability (P2Rank · AlphaFold DB model) 0.853
Direct ligand evidence 0 54 total records
Functional annotation 0 EC 5 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

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 (%)
26.374 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
92.6 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) 0.853
Structure A0A0H3GQV3
Pocket Pocket 1
Druggability (FPocket) 0.602
Structure A0A0H3GQV3
Pocket Pocket 29
ColabFold model
P2Rank 0.759 · Pocket 1
FPocket 0.122 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 26 / 4744 genomes with a hit
Prevalence 0.5%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSRLQQGLKTRQTRFALALKVALLGGVVAFSSAVFAEGLLKEGITPATDASQIPASAKLRKDTVVAGISEPQGIFNPYFFVNGWDENVTNVIFSRLIDWDSQGKLVPGLAESWTVSPDNKVYTIKLRPGLTFSDGSPLTAEDVAFTLTVLLDPKYDGDTDITLANIAGGTDYKAGKADSVSGLKVIDPLTLQVTTTQPGATTLAKIGGPVLSKAWYGKGYQRGNLDYLRSLHGKPLGNGPYVYDKYIPGQEIRFHANSHFYRGTPPTPRFIYRVTNPSTNFQLFQTGETDYDAFTSRPDDIEQLKMLGFANINLYGSSDYSQVEFNVHRPALQDKRVRQALIYGLDRQKLIDVVYQGYGKVAIEPIAPISWAFNAEGVNPYPYDPAQAKKLLDEAGWKAGADGIRAKDGQRLELTLLVSKKVLNDALIPIAKENWRQIGVLLKPQVVDFNALMAQRKAGNYDLASFSTSTLNDPHDGVWDFYSSEAKESGYHNAEVDKLINAGNAVLDIEQRKPIYHQLYKVLADDPPVILLGYREILSASSARVSGFKPDIYNGLTGSLPDVKIVK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Subcellular localization

Localization
Periplasmic

Gene Ontology (GO)

5
  • 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.
  • GO:1904680 Enables the transfer of a peptide from one side of a membrane to the other.
  • GO:0015833 The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, 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.

17 records
Show feature table
Start End DB Term Name
104 486 Pfam PF00496 Bacterial extracellular solute-binding proteins, family 5 Middle
104 486 InterPro IPR000914 Solute-binding protein family 5 domain
63 548 CDD cd00995 PBP2_NikA_DppA_OppA_like
319 534 Gene3D G3DSA:3.10.105.10 -
37 567 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
29 36 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
15 555 PANTHER PTHR30290 PERIPLASMIC BINDING COMPONENT OF ABC TRANSPORTER
15 555 InterPro IPR039424 Solute-binding protein family 5
15 28 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
74 549 Gene3D G3DSA:3.40.190.10 -
13 35 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
20 559 PIRSF PIRSF002741 MppA
20 559 InterPro IPR030678 Peptide/nickel binding protein, MppA-type
1 14 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 36 Phobius SIGNAL_PEPTIDE Signal peptide region
93 225 Gene3D G3DSA:3.90.76.10 -
60 555 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.

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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
0.853
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Surrounding area
Pocket 2 P2Rank #2
0.821
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Surrounding area
Pocket 3 P2Rank #3
0.265
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Surrounding area
Pocket 4 P2Rank #4
0.194
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Surrounding area
Pocket 5 P2Rank #5
0.092
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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 #29
0.602
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_A0A0H3GQV3
AlphaFold DB full sequence Viewing
ColabFold VK055_0456
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
EDT PDB via homolog 292.2 Da · LogP -2.07 · TPSA 155.7 Open detail RCSB PDB
GDS PDB via homolog Detail RCSB PDB
MLI PDB via homolog Detail RCSB PDB
OXL PDB via homolog Detail RCSB PDB
ZINC19364242 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
EDT RCSB PDB Q9AL82 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
GDS RCSB PDB B8F653 612.6 Da LogP -3.88 TPSA 317.6 3 viol. ✓ Clean C(CC(=O)N[C@@H](CSSC[C@@H](C(=O)NCC(=O)O)NC(=O)…
MLI RCSB PDB B8F653 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
OXL RCSB PDB Q0P844 88.0 Da LogP -3.51 TPSA 80.3 ✓ Ro5 ✓ Clean C(=O)(C(=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.