KpKP13 Protein target profile

Na(+)/H(+) antiporter nhaA 1

Accession: KP13_01979

Gene: AHE46417.1 nhaA1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GRG3

Export view

Length 407

Pocket druggability (P2Rank · AlphaFold DB model) 0.691

Direct ligand evidence 0 26 total records

Functional annotation 0 EC 5 GO

Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.69, FPocket 0.82). Use the 3D pocket comparison to verify whether they identify the same site. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.82. This is a computational pocket signal, not binding validation. Review the complete evidence below

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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: 3.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 84.755 Higher values support similarity to known essential genes.
DEG E-value: 0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 87.72 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) 0.691

Structure A0A0H3GRG3

Pocket Pocket 1

Druggability (FPocket) 0.817

Structure A0A0H3GRG3

Pocket Pocket 2

ColabFold model

P2Rank 0.674 · Pocket 1

FPocket 0.936 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 156 / 4744 genomes with a hit

Prevalence 3.3%

Sequence

Primary amino-acid sequence viewer.

MYYAFIELFTNRMKVKVKHLQRFFSSDASGGIVLIIAAALAMVMANTSVTSGLYHSFLETPVQLRVGALEINKNMLLWINDALMAVFFLLIGLEVKRELIQGSLASRRQAVFPVIAALGGMIVPALVYLAFNAQDPVAREGWAIPAATDIAFALGVLALLGSRVPTALKIFLMALAIIDDLGAIVIIALFYTHDLSMLSLGVAAAAIAVLVALNLSGVRRTGIYILVGAVLWTAVLKSGVHATLAGVIVGFMIPLEEKHGKSPAKALEHVLHPWVAFMILPLFAFANAGVSLQGVTLAGLTSLLPLGIMAGLFIGKPLGISLFCWLALKLKWASLPEGTTCKQIMAVGILCGIGFTMSIFIATLAFGSVDPALINWAKLGILIGSVLSAVVGYLILRQRVTDTRLAV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Subcellular localization

Localization: CytoplasmicMembrane

Gene Ontology (GO)

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GO:0006814 The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
GO:0006885 Any process involved in the maintenance of an internal equilibrium of hydrogen ions, thereby modulating the internal pH, within an organism or cell.
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: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).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

45 records

Show feature table

Start	End	DB	Term	Name
301	305	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
170	192	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
32	54	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
109	131	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
17	404	FunFam	G3DSA:1.20.1530.10:FF:000001	Na(+)/H(+) antiporter NhaA
141	163	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
165	169	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
110	131	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
368	372	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
96	109	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
74	96	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
192	197	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
306	328	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
373	395	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
196	218	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
23	45	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
20	404	Hamap	MF_01844	Na(+)/H(+) antiporter NhaA [nhaA].
20	404	InterPro	IPR004670	Na+/H+ antiporter NhaA
75	95	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
218	222	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
373	396	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
231	253	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
397	407	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
143	164	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
23	396	NCBIfam	TIGR00773	Na+/H+ antiporter NhaA
23	396	InterPro	IPR004670	Na+/H+ antiporter NhaA
55	74	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1	31	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
329	343	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
170	191	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
344	367	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
344	366	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
132	142	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
223	253	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
10	401	PANTHER	PTHR30341	SODIUM ION/PROTON ANTIPORTER NHAA-RELATED
10	401	InterPro	IPR004670	Na+/H+ antiporter NhaA
273	295	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
198	217	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
274	300	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
254	273	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
17	403	Gene3D	G3DSA:1.20.1530.10	Na+/H+ antiporter like domain
17	403	InterPro	IPR023171	Na+/H+ antiporter domain superfamily
302	324	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
22	396	Pfam	PF06965	Na+/H+ antiporter 1
22	396	InterPro	IPR004670	Na+/H+ antiporter NhaA

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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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

0.691

Likely same site as FPocket 1 1.9 Å 15 shared residues 100% of smaller site

Show in viewer

Surrounding area

Pocket 2 P2Rank #2

0.502

Show in viewer

Surrounding area

Pocket 3 P2Rank #3

0.491

Show in viewer

Surrounding area

Pocket 4 P2Rank #4

0.254

Likely same site as FPocket 3 1.0 Å 10 shared residues 100% of smaller site

Show in viewer

Surrounding area

Pocket 5 P2Rank #5

0.181

Show in viewer

Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #2

0.817

Show in viewer

Surrounding area

Pocket 2 FPocket #3

0.65

Likely same site as P2Rank 4 1.0 Å 10 shared residues 100% of smaller site

Show in viewer

Surrounding area

Pocket 3 FPocket #1

0.401 Unusual size

Likely same site as P2Rank 1 1.9 Å 15 shared residues 100% of smaller site

Show in viewer

Surrounding area

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1

0.674

Likely same site as FPocket 1 2.4 Å 15 shared residues 94% of smaller site

Show in viewer

Surrounding area

Pocket 2 P2Rank #2

0.595

Show in viewer

Surrounding area

Pocket 3 P2Rank #3

0.479

Show in viewer

Surrounding area

Pocket 4 P2Rank #4

0.303

Likely same site as FPocket 10 1.5 Å 10 shared residues 100% of smaller site

Show in viewer

Surrounding area

Pocket 5 P2Rank #5

0.14

Show in viewer

Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1

0.936 Unusual size

Likely same site as P2Rank 1 2.4 Å 15 shared residues 94% of smaller site

Show in viewer

Surrounding area

Pocket 2 FPocket #10

0.654

Likely same site as P2Rank 4 1.5 Å 10 shared residues 100% of smaller site

Show in viewer

Surrounding area

Pocket 3 FPocket #6

0.358

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_A0A0H3GRG3	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_01979	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.

26 records

Chemistry signal

Bioactivity evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 1 records from similar proteins

Structural ligands 0 0 loaded crystals

Measured bioactivity 1 direct and transferred ChEMBL records

Proposed compounds 25 similarity-based ZINC candidates

Best available ligand signal

1PK ChEMBL via homolog pchembl 6.10 (~794.3 nM) 183.2 Da · LogP 2.21 · TPSA 50.4 Open detail ChEMBL

ZINC2541134 ZINC proposed compound · Tanimoto 0.625 Detail ZINC

ZINC289554 ZINC proposed compound · Tanimoto 0.625 Detail ZINC

ZINC267420 ZINC proposed compound · Tanimoto 0.611 Detail ZINC

ZINC51935 ZINC proposed compound · Tanimoto 0.579 Detail ZINC

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.

No PDB ligands found through similar proteins.

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
1PK ChEMBL	P13738	6.10 ~794.3 nM	183.2 Da LogP 2.21 TPSA 50.4	✓ Ro5	Alert	`c1cc2cccc3c2c(c1)NC(=N3)N`

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
ZINC2541134 ZINC	0.625	202.6 Da LogP 3.49 TPSA 24.4	✓ Ro5	Alert	`Clc1nc2cccc3cccc([nH]1)c32`
ZINC289554 ZINC	0.625	200.3 Da LogP 3.18 TPSA 24.4	✓ Ro5	Alert	`Sc1nc2cccc3cccc([nH]1)c32`
ZINC267420 ZINC	0.611	259.3 Da LogP 3.93 TPSA 50.4	✓ Ro5	Alert	`Nc1ccc(-c2nc3cccc4cccc([nH]2)c43)cc1`
ZINC51935 ZINC	0.579	259.3 Da LogP 3.93 TPSA 50.4	✓ Ro5	Alert	`Nc1cccc(-c2nc3cccc4cccc([nH]2)c43)c1`
ZINC186916 ZINC	0.571	244.3 Da LogP 4.34 TPSA 24.4	✓ Ro5	Alert	`c1ccc(-c2nc3cccc4cccc([nH]2)c43)cc1`
ZINC2491925 ZINC	0.571	236.2 Da LogP 3.86 TPSA 24.4	✓ Ro5	Alert	`FC(F)(F)c1nc2cccc3cccc([nH]1)c32`
ZINC481147 ZINC	0.571	210.3 Da LogP 3.95 TPSA 24.4	✓ Ro5	Alert	`CC(C)c1nc2cccc3cccc([nH]1)c32`
ZINC1436206 ZINC	0.556	212.2 Da LogP 2.38 TPSA 61.7	✓ Ro5	Alert	`O=C(O)c1nc2cccc3cccc([nH]1)c32`
ZINC310678 ZINC	0.541	262.3 Da LogP 4.48 TPSA 24.4	✓ Ro5	Alert	`Fc1ccc(-c2nc3cccc4cccc([nH]2)c43)cc1`
ZINC359231 ZINC	0.541	258.3 Da LogP 4.65 TPSA 24.4	✓ Ro5	Alert	`Cc1ccc(-c2nc3cccc4cccc([nH]2)c43)cc1`
ZINC5645549 ZINC	0.541	210.3 Da LogP 4.10 TPSA 24.4	✓ Ro5	Alert	`CCCc1nc2cccc3cccc([nH]1)c32`
ZINC68675255 ZINC	0.541	245.3 Da LogP 3.74 TPSA 37.3	✓ Ro5	Alert	`c1cc2cccc3[nH]c(-c4ccncc4)nc(c1)c23`
ZINC1607936 ZINC	0.526	225.3 Da LogP 2.86 TPSA 27.6	✓ Ro5	Alert	`CN(C)Cc1nc2cccc3cccc([nH]1)c32`
ZINC481127 ZINC	0.526	258.3 Da LogP 4.54 TPSA 24.4	✓ Ro5	Alert	`c1ccc(Cc2nc3cccc4cccc([nH]2)c43)cc1`
ZINC169972490 ZINC	0.513	262.3 Da LogP 4.48 TPSA 24.4	✓ Ro5	Alert	`Fc1ccccc1-c1nc2cccc3cccc([nH]1)c32`
ZINC169972923 ZINC	0.513	258.3 Da LogP 4.65 TPSA 24.4	✓ Ro5	Alert	`Cc1ccccc1-c1nc2cccc3cccc([nH]1)c32`
ZINC310112 ZINC	0.513	234.3 Da LogP 3.94 TPSA 37.5	✓ Ro5	Alert	`c1coc(-c2nc3cccc4cccc([nH]2)c43)c1`
ZINC359233 ZINC	0.513	272.4 Da LogP 4.93 TPSA 24.4	✓ Ro5	Alert	`c1ccc(CCc2nc3cccc4cccc([nH]2)c43)cc1`
ZINC5037851 ZINC	0.513	234.3 Da LogP 3.07 TPSA 53.1	✓ Ro5	Alert	`c1cc2cccc3[nH]c(-c4cnc[nH]4)nc(c1)c23`
ZINC169972492 ZINC	0.500	262.3 Da LogP 4.48 TPSA 24.4	✓ Ro5	Alert	`Fc1cccc(-c2nc3cccc4cccc([nH]2)c43)c1`
ZINC169972921 ZINC	0.500	258.3 Da LogP 4.65 TPSA 24.4	✓ Ro5	Alert	`Cc1cccc(-c2nc3cccc4cccc([nH]2)c43)c1`
ZINC1718950 ZINC	0.500	274.3 Da LogP 4.03 TPSA 44.6	✓ Ro5	Alert	`O[C@@H](c1ccccc1)c1nc2cccc3cccc([nH]1)c32`
ZINC2036482 ZINC	0.500	274.3 Da LogP 4.03 TPSA 44.6	✓ Ro5	Alert	`O[C@H](c1ccccc1)c1nc2cccc3cccc([nH]1)c32`
ZINC4008197 ZINC	0.500	274.3 Da LogP 4.35 TPSA 33.6	✓ Ro5	Alert	`COc1ccc(-c2nc3cccc4cccc([nH]2)c43)cc1`
ZINC4142739 ZINC	0.500	287.4 Da LogP 4.41 TPSA 27.6	✓ Ro5	Alert	`CN(C)c1ccc(-c2nc3cccc4cccc([nH]2)c43)cc1`

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.

Sequence

UniProt A0A0H3GRG3

Chemistry

ChEMBL 1PK