Protein target profile

VK055_3002

na+/H+ antiporter

Genome: KpATCC43816 Gene: AIK81587.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQ98
Length 548
Pocket druggability 0.977
Direct ligand evidence 0 152 total records
Functional annotation 0 EC 10 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
Hit
Human identity (%)
27.869 Lower values reduce human off-target concern.
Human E-value
5.02e-08
Gut microbiome similarity
2.3% 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.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
86.53 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.977
Structure A0A0H3GQ98
Pocket Pocket 46
P2Rank 0.84
Structure A0A0H3GQ98
Pocket Pocket 1
ColabFold model
FPocket 0.889 · Pocket 41
P2Rank 0.869 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 109 / 4744 genomes with a hit
Prevalence 2.3%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Chemistry

ChEMBL CHEMBL3904640 ChEMBL CHEMBL3973684 ChEMBL CHEMBL5176968 ChEMBL CHEMBL3897251 ChEMBL CHEMBL3990220 ChEMBL CHEMBL5170002 ChEMBL CHEMBL3942614 ChEMBL CHEMBL3967635 ChEMBL CHEMBL3987020 ChEMBL CHEMBL5202545 ChEMBL CHEMBL64889 ChEMBL CHEMBL3968241 ChEMBL CHEMBL3948263 ChEMBL CHEMBL4283742 ChEMBL CHEMBL5845250 ChEMBL CHEMBL3950900 ChEMBL CHEMBL3954388 ChEMBL CHEMBL5861528 ChEMBL CHEMBL3937928 ChEMBL CHEMBL3894457 ChEMBL CHEMBL3921641 ChEMBL CHEMBL3972753 ChEMBL CHEMBL3923266 ChEMBL CHEMBL3932620 ChEMBL CHEMBL3946835 ChEMBL CHEMBL3956501 ChEMBL CHEMBL3967281 ChEMBL CHEMBL3968950 ChEMBL CHEMBL3978001 ChEMBL CHEMBL5183104 ChEMBL CHEMBL5815625 ChEMBL CHEMBL3947060 ChEMBL CHEMBL4279223 ChEMBL CHEMBL1783857 ChEMBL CHEMBL3976345 ChEMBL CHEMBL3979252 ChEMBL CHEMBL3909990 ChEMBL CHEMBL3911722 ChEMBL CHEMBL3972891 ChEMBL CHEMBL5977305 ChEMBL CHEMBL64360 ChEMBL CHEMBL3965836 ChEMBL CHEMBL3914729 ChEMBL CHEMBL3301627 ChEMBL CHEMBL3891308 ChEMBL CHEMBL3908976 ChEMBL CHEMBL3908997 ChEMBL CHEMBL3909231 ChEMBL CHEMBL3913347 ChEMBL CHEMBL3946862 ChEMBL CHEMBL3949556 ChEMBL CHEMBL3954142 ChEMBL CHEMBL3977506 ChEMBL CHEMBL4280644 ChEMBL CHEMBL4289638 ChEMBL CHEMBL5747985 ChEMBL CHEMBL5828476 ChEMBL CHEMBL5846806 ChEMBL CHEMBL5948265 ChEMBL CHEMBL6026005 ChEMBL CHEMBL3911951 ChEMBL CHEMBL4294068 ChEMBL CHEMBL3895338 ChEMBL CHEMBL3901000 ChEMBL CHEMBL3901687 ChEMBL CHEMBL3935315 ChEMBL CHEMBL3951502 ChEMBL CHEMBL3962344 ChEMBL CHEMBL3970997 ChEMBL CHEMBL3972691 ChEMBL CHEMBL3978115 ChEMBL CHEMBL3985915 ChEMBL CHEMBL4284044 ChEMBL CHEMBL4291672 ChEMBL CHEMBL5170188 ChEMBL CHEMBL5202068 ChEMBL CHEMBL5899780 ChEMBL CHEMBL3304485 ChEMBL CHEMBL3906068 ChEMBL CHEMBL3908892 ChEMBL CHEMBL3930643 ChEMBL CHEMBL3941108 ChEMBL CHEMBL3964147 ChEMBL CHEMBL3976660 ChEMBL CHEMBL5562362 ChEMBL CHEMBL5923279 ChEMBL CHEMBL5989386 ChEMBL CHEMBL3943277 ChEMBL CHEMBL1783830 ChEMBL CHEMBL3986598 ChEMBL CHEMBL3910676 ChEMBL CHEMBL3911750 ChEMBL CHEMBL3914902 ChEMBL CHEMBL3932568 ChEMBL CHEMBL3947345 ChEMBL CHEMBL5800421 ChEMBL CHEMBL5828426 ChEMBL CHEMBL5920110 ChEMBL CHEMBL5970664 ChEMBL CHEMBL6021087

Sequence

Primary amino-acid sequence viewer.

MEIFFTILIMTLVVSLSGVVTRVLPFQVPLPLMQIAIGALLAWPTFGLHVEFDPELFLVLFIPPLLFADGWKTPTREFIEHGREILGLALALVVVTVVGIGFLIYWIVPGIPLIPAFALAAVLSPTDAVALSGIVGEGRIPKKIMGILQGEALMNDASGLVSLKFAVAVAMGTMVFTVGGATVEFLKVAIGGVLAGFVVSWSYGRSMRFLSRWGGDEPATQIVLLFLLPFASYLIAEHIGVSGILAAVAAGMTITRSGVMRTAPLAMRLRANSTWAMLEFVFNGMVFLLLGLQLPDILSSSLVAAEADPNVETWMLFTDIILIYAALMLVRFGWLWSMRKLSQRFLKKKPMEFGSWTTRELLISSVAGVRGAITLAGVLSIPLLLPDGNVFPARYELIFLAAGVILFSLFVGVIALPILLRHIESSDNVQQRKEERLARAATADVAIVAIQKMEERLAADTKENIDTQLLTEVSSRVIGNLRRRADGRNDVETSMLEESLERRFRLAALRSERGELYHLRATRQISNETLQKLLHDLDLLEALLIEDQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

10 GO

Gene Ontology (GO)

10
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0006812 The directed movement of a monoatomic cation, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic cations (also called simple cations) are positively charged ions consisting of exactly one atom.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • GO:0015385 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Na+(out) + H+(in) = Na+(in) + H+(out).
  • GO:1902600 The directed movement of a proton across a membrane.
  • GO:0015297 Enables the active transport of a solute across a membrane by a mechanism whereby two or more species are transported in opposite directions in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy. The reaction is: solute A(out) + solute B(in) = solute A(in) + solute B(out).
  • 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:0015386 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: K+(in) + H+(out) = K+(out) + H+(in).
  • GO:0051453 Any process that modulates the internal pH of a cell, corresponding to a change in hydrogen ion concentration.
  • GO:0098719 The directed movement of sodium ions from outside of a cell, across the plasma membrane and into the cytosol.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

43 records
Show feature table
Start End DB Term Name
295 313 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
6 25 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
180 184 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
242 263 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
7 421 Pfam PF00999 Sodium/hydrogen exchanger family
7 421 InterPro IPR006153 Cation/H+ exchanger
275 294 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
74 84 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
26 31 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
338 360 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
237 241 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
56 73 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
264 274 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
175 197 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
109 113 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
185 206 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
115 164 Gene3D G3DSA:6.10.140.1330 -
51 55 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
85 108 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
313 335 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
314 337 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
361 383 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
386 396 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
4 26 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
398 420 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
233 255 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
32 50 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
276 298 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
157 179 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
113 135 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
397 420 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
218 236 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
137 156 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
7 546 NCBIfam TIGR00831 Na+/H+ antiporter
7 546 InterPro IPR004705 Cation/H+ exchanger, CPA1 family, bacteria
1 5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
207 217 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
114 136 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
86 108 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
3 486 PANTHER PTHR10110 SODIUM/HYDROGEN EXCHANGER
3 486 InterPro IPR018422 Cation/H+ exchanger, CPA1 family
361 385 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
421 548 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.

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 · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #46
0.977
Likely same site as P2Rank 1 2.0 Å 15 shared residues 88% of smaller site
Unusual size
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.84
Likely same site as FPocket 46 2.0 Å 15 shared residues 88% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.554
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Surrounding area
Site 3 P2Rank #3
0.452
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Surrounding area
Site 4 P2Rank #4
0.366
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Surrounding area
Site 5 P2Rank #5
0.198
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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_A0A0H3GQ98
AlphaFold DB full sequence Viewing
ColabFold VK055_3002
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.

152 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 102 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
PGT PDB via homolog 751.0 Da · LogP 10.67 · TPSA 148.8 Open detail RCSB PDB
TAM PDB via homolog Detail RCSB PDB
CHEMBL3904640 ChEMBL via homolog · pchembl 9.70 (~0.2 nM) Detail ChEMBL
CHEMBL3973684 ChEMBL via homolog · pchembl 9.30 (~0.5 nM) Detail ChEMBL
CHEMBL5176968 ChEMBL via homolog · pchembl 8.90 (~1.3 nM) Detail ChEMBL

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
PGT RCSB PDB P19634 751.0 Da LogP 10.67 TPSA 148.8 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)O[C@@H](COC(=O)CCCCCCCCCC…
TAM RCSB PDB P19634 163.2 Da LogP -1.17 TPSA 86.7 ✓ Ro5 ✓ Clean C(CO)C(CCO)(CCO)N

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.