Protein target profile

VK055_1987

oxygen-insensitive NAD(P)H nitroreductase

Genome: KpATCC43816 Gene: AIK80593.1 nfnB 3D evidence: Experimental + ColabFold model Metabolism 1 reaction UniProt A6T5Y2
Length 217
Pocket druggability 0.435
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 65 total records
Functional annotation 0 EC 1 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

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
1.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Unknown

Structure confidence

ColabFold pLDDT
98.58 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.435
Structure 8DOR
Pocket Pocket 1
P2Rank 0.03
Structure 8DOR
Pocket Pocket 1
ColabFold model
FPocket 0.262 · Pocket 9
P2Rank 0.005 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 69 / 4744 genomes with a hit
Prevalence 1.5%

Cross-references

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

Structure

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 89.5% of genes in this genome, no human homolog detected.

Relative network centrality 89.5% more central than 89.5% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

Catalyzed reaction

1 reaction 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.

MDIVSVALKRYSTKAFDATKKLTAGEAEQLKTLLQYSPSSTNSQPWHFIVASTDEGKARVAKAASGTYVFNERKILDASHVVVFCAKTAMDDAWLQRVVDQEEADGRFATPDAKAANHKGRTFFADMHRKELKDDDQWMAKQVYLNVGNFLLGVAAMGLDAVPIEGVDFAILDEEFDLKAQGYTSLVVVPVGHHSVEDFNATLPKSRLPQSTTITEI

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

1
  • 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 domains and features

Domain and signature matches imported from InterPro and related databases.

10 records
Show feature table
Start End DB Term Name
2 211 CDD cd02149 NfsB-like
2 211 InterPro IPR033878 Oxygen-insensitive NAD(P)H nitroreductase NfsB-like
3 210 PANTHER PTHR23026 NADPH NITROREDUCTASE
8 193 Pfam PF00881 Nitroreductase family
8 193 InterPro IPR029479 Nitroreductase
1 216 SUPERFAMILY SSF55469 FMN-dependent nitroreductase-like
1 216 InterPro IPR000415 Nitroreductase-like
1 217 Gene3D G3DSA:3.40.109.10 NADH Oxidase
1 217 InterPro IPR000415 Nitroreductase-like
1 217 FunFam G3DSA:3.40.109.10:FF:000002 Oxygen-insensitive NAD(P)H nitroreductase

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 · FPocket

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

Site 1 FPocket #1
0.435
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.03
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.023
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 8DOR
X-ray A Viewing
ColabFold VK055_1987
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.

65 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 15 records from similar proteins
Structural ligands 15 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2HC PDB via homolog 164.2 Da · LogP 1.49 · TPSA 57.5 Open detail RCSB PDB
4HC PDB via homolog Detail RCSB PDB
4NB PDB via homolog Detail RCSB PDB
BEL PDB via homolog Detail RCSB PDB
BEZ 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
2HC RCSB PDB P46072 164.2 Da LogP 1.49 TPSA 57.5 ✓ Ro5 ✓ Clean c1ccc(c(c1)\C=C\C(=O)O)O
4HC RCSB PDB P46072 162.1 Da LogP 1.50 TPSA 50.4 ✓ Ro5 ✓ Clean c1ccc2c(c1)C(=CC(=O)O2)O
4NB RCSB PDB Q01234 167.1 Da LogP 1.29 TPSA 80.4 ✓ Ro5 ✓ Clean c1cc(ccc1C(=O)O)[N+](=O)[O-]
BEL RCSB PDB P38489 510.1 Da LogP 1.60 TPSA 152.8 1 viol. ✓ Clean c1c(c(cc(c1N(CCBr)CCBr)[N+](=O)[O-])[N+](=O)[O-…
BEZ RCSB PDB Q01234 122.1 Da LogP 1.38 TPSA 37.3 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)O
CB1 RCSB PDB P38489 252.2 Da LogP 0.42 TPSA 132.4 ✓ Ro5 ✓ Clean c1c(c(cc(c1N2CC2)[N+](=O)[O-])[N+](=O)[O-])C(=O…
DND RCSB PDB Q01234 665.4 Da LogP -2.42 TPSA 312.5 3 viol. ✓ Clean c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(…
DTC RCSB PDB P38489 336.3 Da LogP 2.21 TPSA 86.7 ✓ Ro5 ✓ Clean c1ccc2c(c1)C(=O)C(C(=O)O2)CC3C(=O)c4ccccc4OC3=O
FLC RCSB PDB P15888 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
MLI RCSB PDB P15888 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
NFZ RCSB PDB P38489 198.1 Da LogP 0.19 TPSA 123.8 ✓ Ro5 ✓ Clean c1cc(oc1\C=N\NC(=O)N)[N+](=O)[O-]
NIO RCSB PDB A0A0U1RIB4 123.1 Da LogP 0.78 TPSA 50.2 ✓ Ro5 ✓ Clean c1cc(cnc1)C(=O)O
SIN RCSB PDB P15888 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
SN2 RCSB PDB P38489 351.1 Da LogP 1.89 TPSA 132.6 ✓ Ro5 ✓ Clean c1c(c(cc(c1N(CCCl)CCCl)[N+](=O)[O-])[N+](=O)[O-…
TLA RCSB PDB P15888 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=O)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.