Protein target profile

VK055_0238

nitrate reductase, alpha subunit

Genome: KpATCC43816 Gene: AIK78866.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GUA4
Length 1247
Pocket druggability 0.983
Metabolic reactions 2
Chokepoint No
Direct ligand evidence 0 63 total records
Functional annotation 1 EC 11 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.

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
3.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
98.3 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 0.983
Structure A0A0H3GUA4
Pocket Pocket 2
P2Rank 0.916
Structure A0A0H3GUA4
Pocket Pocket 1
ColabFold model
FPocket 0.978 · Pocket 2
P2Rank 0.886 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 184 / 4744 genomes with a hit
Prevalence 3.9%

Cross-references

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

Metabolic context

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

Explore metabolic network

Metabolic context: no human homolog detected.

Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Catalyzed reactions

2 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSKFLDRFRYFKQKGETFADGHGQLLNTNRDWEDGYRQRWQHDKIVRSTHGVNCTGSCSWKIYVKNGLVTWETQQTDYPRTRPDLPNHEPRGCPRGASYSWYLYSANRLKYPLMRKRLMKMWREAKVQHSDPVEAWASIIEDADKAKSFKQARGRGGFVRSSWQEVNELIAASNVYTVKTYGPDRVAGFSPIPAMSMVSYASGARYLSLIGGTCLSFYDWYCDLPPASPMTWGEQTDVPESADWYNSSYIIAWGSNVPQTRTPDAHFFTEVRYKGTKTVAITPDYAEIAKLCDLWLAPKQGTDAAMALAMGHVMLREFHLDKPSQYFTDYVRRYTDMPMLVMLEERDGYYAAGRTLRASDLVDSLGQENNPEWKTVAFDEKGDMTVPNGSLGFRWGDKGKWNLEQRDGKTGEEIELRLSLLGSHDEVANVGFPYFGGEGSEHFNKVDLENILLHKLPAKRLQLADGSTALVTTVYDLTMANYGLERGLNDDNCAAGYDEVKAYTPAWAEKITGVSRAHIIRTAREFADNADKTHGRSMIIVGAGLNHWFHLDMNYRGLINMLIFCGCVGQSGGGWAHYVGQEKLRPQTGWQPLAFALDWQRPARHMNSTSYFYNHSSQWRYETVTAQELLSPMADKSRYSGHLIDFNVRAERMGWLPSAPQLGVNPLRIADEAKKAGMTPVDYTVKSLKEGSIRFAAEQPENGKNHPRNLFIWRSNLLGSSGKGHEYMLKYLLGTENGIQGKDLGKQGGVKPEEVEWRDNGLDGKLDLVVTLDFRLSSTCLYSDIVLPTATWYEKDDMNTSDMHPFIHPLSAAVDPAWESKSDWEIYKGIAKKFSEVCVGHLGKETDVVTLPIQHDSAAEMAQPLDVKDWKKGECDLIPGKTAPHIIPVERDYPATYERFTSIGPLLETIGNGGKGIAWNTQSEMDLLRKLNYTKAEGPAKGQPKLETAIDAAEMILTLAPETNGQVAVKAWQALSEITGREHTHLALNKEDEKIRFRDIQAQPRKIISSPTWSGLEDEHVSYNAGYTNVHELIPWRTLSGRQSLYQDHQWMRDFGESLLVYRPPIDTRSVKAVMGEKSNGNPEKALNFLTPHQKWGIHSTYSDNLLMLTLSRGGPIVWMSEADAKDLGIEDNDWIEVFNANGALTARAVVSQRVPAGMTMMYHAQERIVNLPGSEITGQRGGIHNSVTRITPKPTHMIGGYGHLAYGFNYYGTVGSNRDEFVVVRKMKNINWLDGEGNDQVQESVK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 11 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

11
  • GO:0042126 The chemical reactions and pathways involving nitrates, inorganic or organic salts and esters of nitric acid.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0043546 Binding to a molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) coordinated by one or two molybdopterin ligands.
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0008940 Catalysis of the reaction: nitrite + acceptor = nitrate + reduced acceptor.
  • GO:0009325 An enzyme complex that catalyzes the formation of nitrate from nitrite with the concomitant reduction of an acceptor.
  • 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:0046872 Binding to a metal ion.
  • GO:0160182 Catalysis of the reaction: a quinol + nitrate = a quinone + H2O + nitrite.
  • GO:0019645 A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors other than oxygen to generate a transmembrane electrochemical gradient.
  • 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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

30 records
Show feature table
Start End DB Term Name
44 1245 Gene3D G3DSA:3.40.50.12440 -
1087 1226 CDD cd02776 MopB_CT_Nitrate-R-NarG-like
1087 1226 InterPro IPR037943 Nitrate reductase alpha subunit-like, MopB domain
777 794 ProSitePatterns PS00490 Prokaryotic molybdopterin oxidoreductases signature 2.
777 794 InterPro IPR006655 Molybdopterin oxidoreductase, prokaryotic, conserved site
48 66 ProSitePatterns PS00551 Prokaryotic molybdopterin oxidoreductases signature 1.
48 66 InterPro IPR027467 Molybdopterin oxidoreductase, molybdopterin cofactor binding site
43 107 ProSiteProfiles PS51669 Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.
43 107 InterPro IPR006963 Molybdopterin oxidoreductase, 4Fe-4S domain
2 1235 NCBIfam TIGR01580 nitrate reductase subunit alpha
2 1235 InterPro IPR006468 Nitrate reductase, alpha subunit
1087 1202 Pfam PF01568 Molydopterin dinucleotide binding domain
1087 1202 InterPro IPR006657 Molybdopterin dinucleotide-binding domain
43 105 SMART SM00926 Molybdop_Fe4S4_2
43 105 InterPro IPR006963 Molybdopterin oxidoreductase, 4Fe-4S domain
1125 1152 ProSitePatterns PS00932 Prokaryotic molybdopterin oxidoreductases signature 3.
1125 1152 InterPro IPR006655 Molybdopterin oxidoreductase, prokaryotic, conserved site
6 1226 PANTHER PTHR43105 RESPIRATORY NITRATE REDUCTASE
43 834 CDD cd02750 MopB_Nitrate-R-NarG-like
44 1236 FunFam G3DSA:3.40.50.12440:FF:000001 Nitrate reductase subunit alpha
2 43 FunFam G3DSA:4.10.1200.10:FF:000001 Respiratory nitrate reductase subunit alpha
1082 1235 SUPERFAMILY SSF50692 ADC-like
1082 1235 InterPro IPR009010 Aspartate decarboxylase-like domain superfamily
108 833 Pfam PF00384 Molybdopterin oxidoreductase
108 833 InterPro IPR006656 Molybdopterin oxidoreductase
4 1070 SUPERFAMILY SSF53706 Formate dehydrogenase/DMSO reductase, domains 1-3
2 43 Gene3D G3DSA:4.10.1200.10 nitrate reductase tail
2 43 InterPro IPR044906 Nitrate reductase, alpha subunit, N-terminal domain superfamily
3 40 Pfam PF14710 Respiratory nitrate reductase alpha N-terminal
3 40 InterPro IPR028189 Nitrate reductase, alpha subunit, N-terminal

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 #2
0.983
Likely same site as P2Rank 3 0.4 Å 30 shared residues 94% of smaller site
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Surrounding area
Site 2 FPocket #1
0.966
Likely same site as P2Rank 2 0.3 Å 31 shared residues 100% of smaller site
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Surrounding area
Site 3 FPocket #8
0.701
Likely same site as P2Rank 5 2.6 Å 10 shared residues 83% of smaller site
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Surrounding area
Site 4 FPocket #58
0.555
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
0.916
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Surrounding area
Site 2 P2Rank #2
0.863
Likely same site as FPocket 1 0.3 Å 31 shared residues 100% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.826
Likely same site as FPocket 2 0.4 Å 30 shared residues 94% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.34
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Surrounding area
Site 5 P2Rank #5
0.202
Likely same site as FPocket 8 2.6 Å 10 shared residues 83% of smaller site
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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_A0A0H3GUA4
AlphaFold DB full sequence Viewing
ColabFold VK055_0238
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.

63 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 13 records from similar proteins
Structural ligands 13 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2MD PDB via homolog 742.6 Da · LogP -2.53 · TPSA 346.6 Open detail RCSB PDB
2MO PDB via homolog Detail RCSB PDB
3PH PDB via homolog Detail RCSB PDB
6MO PDB via homolog Detail RCSB PDB
AGA 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
2MD RCSB PDB O87948 742.6 Da LogP -2.53 TPSA 346.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=…
2MO RCSB PDB O87948 127.9 Da LogP -0.24 TPSA 34.1 ✓ Ro5 ✓ Clean O=[Mo]=O
3PH RCSB PDB P09152 705.0 Da LogP 12.07 TPSA 119.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O…
6MO RCSB PDB P09152 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo+6]
AGA RCSB PDB P09152 455.5 Da LogP 1.85 TPSA 151.7 ✓ Ro5 ✓ Clean CCCCCCCC(=O)O[C@H](COC(=O)CCCC)COP(=O)([O-])OC[…
BSY RCSB PDB G8QM55 128.0 Da LogP -2.25 TPSA 60.4 ✓ Ro5 ✓ Clean O[Se](=O)[O-]
F3S RCSB PDB P09152 295.8 Da LogP 2.59 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]2S[Fe]3[S]2[Fe]1S3
H2S RCSB PDB Q72EJ1 34.1 Da LogP 0.11 TPSA 0.0 ✓ Ro5 ✓ Clean S
MD1 RCSB PDB P09152 740.6 Da LogP -2.13 TPSA 358.0 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
MGD RCSB PDB P09152 740.6 Da LogP -2.06 TPSA 346.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=…
MO RCSB PDB P09152 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo]
PCI RCSB PDB P09152 266.3 Da LogP 4.66 TPSA 20.2 ✓ Ro5 ✓ Clean c1(c(c(c(c(c1Cl)Cl)Cl)Cl)Cl)O
W RCSB PDB Q72EJ1 183.8 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [W+6]

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.