Protein target profile

PA3876

nitrite extrusion protein 2

Genome: NC_002516.2

Gene: PA3876 narK2 3D evidence: AlphaFold DB model UniProt Q9HXD4
Length 468
Pocket druggability 0.712
Ligand records 52
EC / GO 0 / 10
Target summary

Promising target candidate with multiple supporting evidence streams.

5 signals
How to read 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 TPW 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.

Overview

Basic information about this protein and its source genome.

Accession
PA3876
Gene
PA3876 narK2
Status
annotated
Amino acids
468
3D evidence
AlphaFold DB model

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
Hit
Essential (DEG)
Y
Localization
CytoplasmicMembrane

Selected pocket evidence

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 0.712
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MGMIANTQLKAARGPLLLDWRPEDPEFWARNGKRIASRNLWISIPALLLAFAVWMIWSTVTVRLNSAGFAFSNDQLFLLAALPSISGATLRVFYSFMVPIFGGRRWTALSTASMLIPCIWLGFAVQDPSTPYWVFALIALLCGFGGGNFASSMSNISFFYPKSQQGTALGLNAGLGNLGVSVMQFAVPLAVAGGLFGAFGGEPQQLGDGGRLWLQNAGWIWVPFIAVVSVAAWFGMNDIADAKASFRDQAVIFKRKHNWLMCWLYVATFGSFIGFSAGFAMLSKTQFPDVNPLQYAFLGPLVGALSRPLGGWLADKFGGARITLWNYALMIGGVFAVIAFLPGDGGQGNFFGFLGAFILLFFFAGIGNGSTFRMIPVIFRNEWARRVRDGQADEAGAARNASMESAAVIGFSAAIGAFGGFFIPKAFGTSLHMTGSAEGALYVFIAYYLSCIVATWWWYARKGAESPC

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

10 GO

Gene Ontology (GO)

10
  • 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:0015112 Enables the transfer of nitrate ions (NO3-) from one side of a membrane to the other.
  • GO:0015113 Enables the transfer of nitrite (NO2-) ions from one side of a membrane to the other.
  • GO:0015291 Enables the transfer of a solute from one side of a membrane to the other, up its concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a chemiosmotic source of energy, not direct ATP coupling. Secondary active transporters include symporters and antiporters.
  • GO:0042128 The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances.
  • GO:0015706 The directed movement of nitrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0022857 Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other.
  • GO:0015707 The directed movement of nitrite into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

Sequence Features

Domain/signature hits from InterPro and related databases.

50 records
Show feature table
Start End DB Term Name
40 57 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
76 98 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
438 460 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
428 438 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
348 366 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
200 218 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
324 342 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
39 61 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
292 314 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
219 239 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
282 292 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
260 282 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
343 347 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
169 191 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
217 239 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
3 465 FunFam G3DSA:1.20.1250.20:FF:000024 Nitrite extrusion protein NarK
21 460 SUPERFAMILY SSF103473 MFS general substrate transporter
21 460 InterPro IPR036259 MFS transporter superfamily
105 124 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
106 125 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
406 427 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
95 105 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
77 94 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
58 76 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
240 259 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
293 312 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
439 459 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
3 465 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains
3 465 InterPro IPR036259 MFS transporter superfamily
40 457 CDD cd17341 MFS_NRT2_like
40 457 InterPro IPR044772 Nitrate transporter
171 199 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
460 468 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
38 420 NCBIfam TIGR00886 NarK family nitrate/nitrite MFS transporter
38 420 InterPro IPR004737 Nitrate transporter NarK/NarU-like
151 170 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
260 281 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
323 340 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
126 130 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
46 378 Pfam PF07690 Major Facilitator Superfamily
46 378 InterPro IPR011701 Major facilitator superfamily
134 156 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 39 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
11 459 PANTHER PTHR23515 HIGH-AFFINITY NITRATE TRANSPORTER 2.3
11 459 InterPro IPR044772 Nitrate transporter
367 405 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
131 150 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
406 423 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
350 372 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
313 323 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.

3D visualization script Full viewer

Loading 3D structure...

Legend High Medium Low

Structural evidence

0 + 1

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 PA3876
AlphaFold DB full sequence Viewing
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 #2
0.695
Unusual size
Show in viewer
Site 2 FPocket #9
0.626
Show in viewer
Site 3 FPocket #6
0.249
Show in viewer

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.

52 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 52 via homologs
Structural ligands 2 0 loaded crystals
Bioactive compounds 0 50 ZINC proposed compounds
Drug-like & clean 51 0 PAINS alerts
Best available ligand signal
OLA PDB via homolog 282.5 Da · LogP 6.11 · TPSA 37.3 Open detail RCSB PDB
Detail RCSB PDB OLA PDB via homolog
Detail RCSB PDB OLC PDB via homolog
Detail ZINC ZINC1501016272 ZINC proposed compound · Tanimoto 1.000
Detail ZINC ZINC1501016273 ZINC proposed compound · Tanimoto 1.000

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
OLA RCSB PDB P10903 282.5 Da LogP 6.11 TPSA 37.3 1 viol. ✓ Clean CCCCCCCC\C=C/CCCCCCCC(=O)O
OLC RCSB PDB P10903 356.5 Da LogP 4.92 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H](CO)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.