Protein target profile

PA1174

nitrate reductase catalytic subunit

Genome: NC_002516.2

Gene: PA1174 napA 3D evidence: AlphaFold DB model UniProt Q9I4G3
Length 829
Pocket druggability 0.712
Ligand records 60
EC / GO 1 / 14
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
PA1174
Gene
PA1174 napA
Status
annotated
Amino acids
829
3D evidence
AlphaFold DB model

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
Periplasmic

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.

MNSPRPTPPPFAAAAAGLPILVRASNLVTEADVTSLVWNKAPCRFCGTGCSVMVATRDGQVVATHGDIKAEVNRGINCVKGYFLSKIMYGSDRLTRPLLRMKDGKFDKQGEFQPISWEQAFDIMAEKFKAALKAKGPESVGMFGSGQWTVWEGYAANKLFKAGLRSNNIDPNARHCMASAVMGFMRSFGMDEPMGCYDDIEATDSFVLWGSNMAEMHPVLWSRVTDRRLSAPQVKVAVLSTFEHRSFELADLPMVFKPQTDLIILNYIANHIIESGAVNRDFVERHVRFAHGAEDIGYGLRPDDPLEKKAKNADKANTWSDIDFKAFAEFVKPYTLERTARESGVPAERLKALAELYADPKRKVVSFWTMGFNQHTRGVWANNLIYNIHLLTGKISEPGNSPFSLTGQPSACGTAREVGTFSHRLPADLVVTNPKHRETAEKIWKVPAGTIQEKVGFHAVQQSRMLKDGVLNVYWTQVSNNMQAGPNVMQEVLPGWRNPDNFVIVSDVYPTVSAQAADLILPSAMWVEKEGAFGNAERRTQFWHQLVKAPGEAKSDLWQLVEFSKRFTTDEVWPAELLAKAPELKGKTLYDVLFRNGQVDRFPASDLAKGYANDEVDAFGFYIQKGLFEEYAAFGRGHGHDLAPFDAYHEARGLRWPVVDGKETRWRYREGYDPYVSKGSGVQFYGYPDKKAIVFALPYEPPAEAPDQDYPFWLATGRVLEHWHTGSMTARVPELYKAVPDALVYMHPEDARQLKLRRGSEVKVVSRRGEIRARVETRGRNKPPQGLVFVPFFDANKLINKVTLDATDPISKQTDYKKCAVRIELLNLA

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 14 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

14
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0009325 An enzyme complex that catalyzes the formation of nitrate from nitrite with the concomitant reduction of an acceptor.
  • GO:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
  • 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:0009055 A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways.
  • GO:0005506 Binding to an iron (Fe) ion.
  • GO:0030151 Binding to a molybdenum ion (Mo).
  • 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:0050140 Catalysis of the reaction: 2 Fe(II)-[cytochrome] + nitrate + 2 H+ = 2 Fe(III)-[cytochrome] + nitrite + H2O.
  • GO:0008940 Catalysis of the reaction: nitrite + acceptor = nitrate + reduced acceptor.
  • GO:0045333 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration).
  • GO:0006777 The chemical reactions and pathways resulting in the formation of the Mo-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear molybdenum (Mo) ion coordinated by one or two molybdopterin ligands.
  • 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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

33 records
Show feature table
Start End DB Term Name
685 824 SUPERFAMILY SSF50692 ADC-like
685 824 InterPro IPR009010 Aspartate decarboxylase-like domain superfamily
1 10 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
12 824 NCBIfam TIGR01706 periplasmic nitrate reductase subunit alpha
12 824 InterPro IPR010051 Periplasmic nitrate reductase, large subunit
93 566 Pfam PF00384 Molybdopterin oxidoreductase
93 566 InterPro IPR006656 Molybdopterin oxidoreductase
41 58 ProSitePatterns PS00551 Prokaryotic molybdopterin oxidoreductases signature 1.
41 58 InterPro IPR027467 Molybdopterin oxidoreductase, molybdopterin cofactor binding site
36 90 SMART SM00926 Molybdop_Fe4S4_2
36 90 InterPro IPR006963 Molybdopterin oxidoreductase, 4Fe-4S domain
31 829 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
93 621 Gene3D G3DSA:3.40.50.740 -
38 89 Pfam PF04879 Molybdopterin oxidoreductase Fe4S4 domain
38 89 InterPro IPR006963 Molybdopterin oxidoreductase, 4Fe-4S domain
702 826 FunFam G3DSA:2.40.40.20:FF:000005 Periplasmic nitrate reductase
32 643 SUPERFAMILY SSF53706 Formate dehydrogenase/DMSO reductase, domains 1-3
1 826 Hamap MF_01630 Periplasmic nitrate reductase [napA].
1 826 InterPro IPR010051 Periplasmic nitrate reductase, large subunit
23 30 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
702 825 Gene3D G3DSA:2.40.40.20 -
11 22 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 30 Phobius SIGNAL_PEPTIDE Signal peptide region
712 820 Pfam PF01568 Molydopterin dinucleotide binding domain
712 820 InterPro IPR006657 Molybdopterin dinucleotide-binding domain
36 92 ProSiteProfiles PS51669 Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.
36 92 InterPro IPR006963 Molybdopterin oxidoreductase, 4Fe-4S domain
40 702 CDD cd02754 MopB_Nitrate-R-NapA-like
37 664 Gene3D G3DSA:3.30.200.210 -
37 825 PANTHER PTHR43105 RESPIRATORY NITRATE REDUCTASE
709 824 CDD cd02791 MopB_CT_Nitrate-R-NapA-like
709 824 InterPro IPR041957 Nitrate reductase NapA-like, molybdopterin-binding domain
172 701 Gene3D G3DSA:3.40.228.10 Dimethylsulfoxide Reductase, domain 2

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

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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 PA1174
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 #1
0.712
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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.

60 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 60 via homologs
Structural ligands 10 0 loaded crystals
Bioactive compounds 0 50 ZINC proposed compounds
Drug-like & clean 16 0 PAINS alerts
Best available ligand signal
2MD PDB via homolog 742.6 Da · LogP -2.53 · TPSA 346.6 Open detail RCSB PDB
Detail RCSB PDB 2MD PDB via homolog
Detail RCSB PDB 4MO PDB via homolog
Detail RCSB PDB 6MO PDB via homolog
Detail RCSB PDB FES PDB via homolog

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 P07658 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@@](=…
4MO RCSB PDB P07658 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo+4]
6MO RCSB PDB D5AQH0 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo+6]
FES RCSB PDB D5AQH0 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
H2S RCSB PDB D5AQH0 34.1 Da LogP 0.11 TPSA 0.0 ✓ Ro5 ✓ Clean S
LCP RCSB PDB P81186 99.4 Da LogP -4.76 TPSA 92.2 ✓ Ro5 ✓ Clean [O-]Cl(=O)(=O)=O
MGD RCSB PDB P81186 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 P81186 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo]
MOS RCSB PDB P39185 161.0 Da LogP 0.14 TPSA 34.1 ✓ Ro5 ✓ Clean O=[Mo](=O)S
NO2 RCSB PDB P07658 46.0 Da LogP 0.25 TPSA 52.5 ✓ Ro5 ✓ Clean N(=O)[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.