KpATCC43816 Protein target profile

yrbG CaCA transporter

Accession: VK055_3871

Gene: AIK82421.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GW74
Length 325
Pocket druggability (P2Rank · AlphaFold DB model) 0.239
Direct ligand evidence 0 56 total records
Functional annotation 0 EC 6 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
Hit
Human identity (%)
47.368 Lower values reduce human off-target concern.
Human E-value
2.81e-07
Gut microbiome similarity
2.0% 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
90.33 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) 0.239
Structure A0A0H3GW74
Pocket Pocket 1
Druggability (FPocket) 0.722
Structure A0A0H3GW74
Pocket Pocket 7
ColabFold model
P2Rank 0.709 · Pocket 1
FPocket 0.817 · Pocket 15
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 95 / 4744 genomes with a hit
Prevalence 2.0%

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.

MLLATALLIIGLLLVVYSADRLVYAASILCRMLGIPPLIIGMTVVSIGTSLPEIMVATAASLHGQTDLAVGTALGSNITNILLILGLAALLRPFTVHSDILRRELPLMLLVSVLAGLVLYDGQLTRLDGLFLLALALLWLLFTIKIARLAERQGSDSLTREQLAELPREGSLPVALLWLGVAMIVMPMATRMVVDNSTVLANYFAISELTVGLTVVAIGTSLPELATAIAGARKGEDDIAIGNIIGANILNIALVLGLPALIAPGSFATEAFTRDYGVMLLVSLIFAVLCWRRQQQPGRLVGALLVGGFVVWLAMLFWTAPLFVE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

6
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0005262 Enables the energy-independent facilitated diffusion of a calcium ion through a transmembrane aqueous pore or channel.
  • GO:0008273 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Ca2+(in) + K+(in) + Na+(out) = Ca2+(out) + K+(out) + Na+(in).
  • GO:0006874 A homeostatic process involved in the maintenance of a steady state level of calcium ions within a cell.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

44 records
Show feature table
Start End DB Term Name
265 275 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
68 90 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
2 17 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
200 219 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
2 312 NCBIfam TIGR00367 calcium/sodium antiporter
2 312 InterPro IPR004481 Sodium/potassium/calcium exchanger
26 34 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
105 122 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
2 151 PANTHER PTHR10846 SODIUM/POTASSIUM/CALCIUM EXCHANGER
2 151 InterPro IPR004481 Sodium/potassium/calcium exchanger
239 264 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
35 319 Gene3D G3DSA:1.20.1420.30 -
35 319 InterPro IPR044880 NCX, central ion-binding domain superfamily
35 56 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
239 261 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
105 124 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
129 150 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
91 104 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
18 25 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
300 324 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 18 SignalP_EUK SignalP-TM SignalP-TM
1 25 Phobius SIGNAL_PEPTIDE Signal peptide region
172 194 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
4 26 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
189 199 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
300 322 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
276 293 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
129 151 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
123 128 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
170 188 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
204 226 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
33 55 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
325 325 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
276 294 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
220 238 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
295 299 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
70 92 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
57 67 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
151 169 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
176 317 Pfam PF01699 Sodium/calcium exchanger protein
176 317 InterPro IPR004837 Sodium/calcium exchanger membrane region
4 144 Pfam PF01699 Sodium/calcium exchanger protein
4 144 InterPro IPR004837 Sodium/calcium exchanger membrane region

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
0.239
Likely same site as FPocket 4 5.3 Å 8 shared residues 62% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.086
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Surrounding area
Pocket 3 P2Rank #3
0.033
Likely same site as FPocket 7 5.2 Å 8 shared residues 89% of smaller site
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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 #7
0.722 Unusual size
Likely same site as P2Rank 3 5.2 Å 8 shared residues 89% of smaller site
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Surrounding area
Pocket 2 FPocket #4
0.414 Unusual size
Likely same site as P2Rank 1 5.3 Å 8 shared residues 62% of smaller site
Show in viewer
Surrounding area
Pocket 3 FPocket #5
0.404
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_A0A0H3GW74
AlphaFold DB full sequence Viewing
ColabFold VK055_3871
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.

56 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 6 records from similar proteins
Structural ligands 6 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
MYC PDB via homolog 318.2 Da · LogP 1.69 · TPSA 151.6 Open detail RCSB PDB
MYS PDB via homolog Detail RCSB PDB
OLC PDB via homolog Detail RCSB PDB
P3G PDB via homolog Detail RCSB PDB
PE8 PDB via homolog Detail RCSB PDB

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
MYC RCSB PDB Q57556 318.2 Da LogP 1.69 TPSA 151.6 1 viol. Alert c1c(cc(c(c1O)O)O)C2=C(C(=O)c3c(cc(cc3O2)O)O)O
MYS RCSB PDB Q57556 212.4 Da LogP 6.10 TPSA 0.0 1 viol. ✓ Clean CCCCCCCCCCCCCCC
OLC RCSB PDB Q57556 356.5 Da LogP 4.92 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H](CO)O
P3G RCSB PDB Q57556 250.3 Da LogP 1.11 TPSA 46.2 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCC
PE8 RCSB PDB Q57556 370.4 Da LogP -0.91 TPSA 105.1 ✓ Ro5 ✓ Clean C(COCCOCCOCCOCCOCCOCCOCCO)O
TOE RCSB PDB Q57556 164.2 Da LogP -0.34 TPSA 47.9 ✓ Ro5 ✓ Clean COCCOCCOCCO

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.