KpATCC43816 Protein target profile

pentaerythritol tetranitrate reductase

Accession: VK055_0488

Gene: onr AIK79111.1 3D evidence: Experimental + ColabFold model Metabolism Not in network UniProt A0A0H3GQS4
Length 365
Pocket druggability (P2Rank · Experimental) 0.868
Direct ligand evidence 0 70 total records
Functional annotation 0 EC 4 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
2.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
37.681 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
97.85 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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) 0.868
Structure 7TMB
Pocket Pocket 1
Druggability (FPocket) 0.915
Structure 7TMB
Pocket Pocket 3
ColabFold model
P2Rank 0.9 · Pocket 1
FPocket 0.491 · Pocket 4
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 105 / 4744 genomes with a hit
Prevalence 2.2%

Metabolic context

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

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSEAKLFSPLKVGAVTVPNRVFMAPLTRLRSIEPGDIPTPLMGEYYRQRASSGLIITEATQISAQAKGYAGAPGLHSPEQIAAWQKITAGVHAENGHIAVQLWHTGRISHSSLQPGGAAPVAPSALSAGTRTSLRDENGHAIRVDTSMPRALETAEIPGIVNDFRQAVGNARDAGFDLVELHSAHGYLLHQFLSPSANQRTDQYGGSVENRARLVLEVVDAVSQEWSAERIGIRVSPIGSFQNVDNGPNEEEDALYLISELAKRGIAYLHMSEPDWAGGKPYSEAFRQKVRDRFPGVIIGAGAYTVEKANDLINKGLIDAVAFGRDYIANPDLVARLQKKAPLNPQRPESFYGGGAEGYTDYPTL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

4
  • GO:0010181 Binding to flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
  • 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0016628 Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces NAD or NADP.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

9 records
Show feature table
Start End DB Term Name
5 345 CDD cd02933 OYE_like_FMN
4 364 PANTHER PTHR22893 NADH OXIDOREDUCTASE-RELATED
4 364 InterPro IPR045247 Oxidoreductase Oye-like
3 365 Gene3D G3DSA:3.20.20.70 Aldolase class I
3 365 InterPro IPR013785 Aldolase-type TIM barrel
3 365 FunFam G3DSA:3.20.20.70:FF:000059 N-ethylmaleimide reductase, FMN-linked
5 344 Pfam PF00724 NADH:flavin oxidoreductase / NADH oxidase family
5 344 InterPro IPR001155 NADH:flavin oxidoreductase/NADH oxidase, N-terminal
4 364 SUPERFAMILY SSF51395 FMN-linked oxidoreductases

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

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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 · P2Rank

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

Pocket 1 P2Rank #1
0.868
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.023
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #3
0.915
Show in viewer
Surrounding area
All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 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
PDB 7TMB
X-ray 2.10 Å A,B,C,D,E,F
100.0% 1-365
Viewing
ColabFold VK055_0488
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.

70 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 20 records from similar proteins
Structural ligands 20 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
1L5 PDB via homolog 163.2 Da · LogP 2.32 · TPSA 43.1 Open detail RCSB PDB
8OZ PDB via homolog Detail RCSB PDB
A2Q PDB via homolog Detail RCSB PDB
ANB PDB via homolog Detail RCSB PDB
BEN 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
1L5 RCSB PDB O31246 163.2 Da LogP 2.32 TPSA 43.1 ✓ Ro5 ✓ Clean C/C(=C\N(=O)=O)/c1ccccc1
8OZ RCSB PDB O31246 148.2 Da LogP 1.78 TPSA 37.3 ✓ Ro5 ✓ Clean C=C(c1ccccc1)C(=O)O
A2Q RCSB PDB P71278 96.1 Da LogP 1.30 TPSA 17.1 ✓ Ro5 ✓ Clean C1CC=CC(=O)C1
ANB RCSB PDB P71278 284.4 Da LogP 3.86 TPSA 34.1 ✓ Ro5 ✓ Clean C[C@]12CC[C@H]3[C@H]([C@@H]1CCC2=O)CCC4=CC(=O)C…
BEN RCSB PDB K9TVC9 120.2 Da LogP 0.97 TPSA 49.9 ✓ Ro5 ✓ Clean [H]/N=C(\c1ccccc1)/N
DNF RCSB PDB P71278 184.1 Da LogP 1.21 TPSA 106.5 ✓ Ro5 ✓ Clean c1cc(c(cc1[N+](=O)[O-])[N+](=O)[O-])O
FNR RCSB PDB P71278 458.4 Da LogP -0.93 TPSA 208.4 1 viol. ✓ Clean Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C…
HBA RCSB PDB O31246 122.1 Da LogP 1.20 TPSA 37.3 ✓ Ro5 ✓ Clean c1cc(ccc1C=O)O
KSW RCSB PDB M2XAQ9 94.1 Da LogP 1.07 TPSA 17.1 ✓ Ro5 ✓ Clean CC1=CC=CC1=O
NYH RCSB PDB P71278 127.1 Da LogP 1.72 TPSA 43.1 ✓ Ro5 ✓ Clean C1CCC(=CC1)[N+](=O)[O-]
P7Y RCSB PDB P71278 165.1 Da LogP 1.64 TPSA 63.4 ✓ Ro5 ✓ Clean c1ccc(c(c1)/C=C/[N+](=O)[O-])O
P80 RCSB PDB P71278 165.1 Da LogP 1.64 TPSA 63.4 ✓ Ro5 ✓ Clean c1cc(cc(c1)O)/C=C/[N+](=O)[O-]
P81 RCSB PDB P71278 165.1 Da LogP 1.64 TPSA 63.4 ✓ Ro5 ✓ Clean c1cc(ccc1/C=C/[N+](=O)[O-])O
PDN RCSB PDB P71278 358.4 Da LogP 3.16 TPSA 94.8 ✓ Ro5 ✓ Clean C[C@]12CC(=O)[C@H]3[C@H]([C@@H]1CC[C@@]2(C(=CO)…
STR RCSB PDB P71278 314.5 Da LogP 4.72 TPSA 34.1 ✓ Ro5 ✓ Clean CC(=O)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CCC4=…
TNF RCSB PDB P71278 229.1 Da LogP 1.12 TPSA 149.7 ✓ Ro5 ✓ Clean c1c(cc(c(c1[N+](=O)[O-])O)[N+](=O)[O-])[N+](=O)…
TNL RCSB PDB P71278 227.1 Da LogP 1.72 TPSA 129.4 ✓ Ro5 ✓ Clean Cc1c(cc(cc1[N+](=O)[O-])[N+](=O)[O-])[N+](=O)[O…
TXD RCSB PDB Q51990 667.5 Da LogP -3.30 TPSA 317.6 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
U5N RCSB PDB M2XAQ9 98.1 Da LogP 0.49 TPSA 26.3 ✓ Ro5 ✓ Clean C[C@@H]1C=CC(=O)O1
U6W RCSB PDB M2XAQ9 98.1 Da LogP 0.84 TPSA 26.3 ✓ Ro5 ✓ Clean CC1=CCC(=O)O1

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.

Structure