Protein target profile
VK055_1987
oxygen-insensitive NAD(P)H nitroreductase
Promising target candidate with multiple supporting evidence streams.
Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.
Main supporting evidence
Risks to review
Evidence coverage
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 structureThe 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.
Cross-references
External database identifiers for this protein, its structures, ligands, and metabolic reactions.
Sequence
Structure
Pathways
Sequence
Primary amino-acid sequence viewer.
MDIVSVALKRYSTKAFDATKKLTAGEAEQLKTLLQYSPSSTNSQPWHFIVASTDEGKARVAKAASGTYVFNERKILDASHVVVFCAKTAMDDAWLQRVVDQEEADGRFATPDAKAANHKGRTFFADMHRKELKDDDQWMAKQVYLNVGNFLLGVAAMGLDAVPIEGVDFAILDEEFDLKAQGYTSLVVVPVGHHSVEDFNATLPKSRLPQSTTITEI
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
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.
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.
How colors and pocket overlays are used
Pocket details Inspect a specific pocket, or open the full viewer
- Method
- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
Selecting a pocket opens its details and centers the viewer without clearing other active layers. Use Focus this pocket when you want to hide the rest; use Surface for the wider residue environment.
Binding pockets · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Residue sets
All structural evidence
Structural evidence
1 + 1Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the 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.
Structural ligand evidence is available for this target.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.
No PDB structure with a co-crystallized ligand found for this exact protein.
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.
| 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
|
Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL bioactivity data found for this exact protein.
Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL hits found through similar proteins.
Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).
| Ligand | Tanimoto | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|
| ZINC4475105 ZINC | 1.000 | 252.2 Da LogP 0.42 TPSA 132.4 | ✓ Ro5 | ✓ Clean |
NC(=O)c1cc(N2CC2)c([N+](=O)[O-])cc1[N+](=O)[O-]
|
| ZINC168904 ZINC | 0.875 | 243.2 Da LogP 2.96 TPSA 80.4 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(-c2ccc([N+](=O)[O-])cc2)cc1
|
| ZINC281559 ZINC | 0.875 | 271.2 Da LogP 2.52 TPSA 97.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(C(=O)c2ccc([N+](=O)[O-])cc2)cc1
|
| ZINC3269660 ZINC | 0.824 | 254.2 Da LogP 2.45 TPSA 71.4 | ✓ Ro5 | Alert |
O=C(O)c1ccc(C(=O)C(=O)c2ccccc2)cc1
|
| ZINC238950253 ZINC | 0.785 | 744.4 Da LogP -2.90 TPSA 364.8 | 3 viol. | ✓ Clean |
NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO[P@](=O)(O)O[P@…
|
| ZINC238950256 ZINC | 0.785 | 744.4 Da LogP -2.90 TPSA 364.8 | 3 viol. | ✓ Clean |
NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO[P@](=O)(O)O[P@…
|
| ZINC238950259 ZINC | 0.785 | 744.4 Da LogP -2.90 TPSA 364.8 | 3 viol. | ✓ Clean |
NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO[P@](=O)(O)O[P@…
|
| ZINC238950261 ZINC | 0.785 | 744.4 Da LogP -2.90 TPSA 364.8 | 3 viol. | ✓ Clean |
NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO[P@](=O)(O)O[P@…
|
| ZINC1675827 ZINC | 0.778 | 307.3 Da LogP 2.13 TPSA 114.6 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(S(=O)(=O)c2ccc([N+](=O)[O-])cc2)cc1
|
| ZINC19806403 ZINC | 0.778 | 275.3 Da LogP 3.44 TPSA 80.4 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(Sc2ccc([N+](=O)[O-])cc2)cc1
|
| ZINC235952 ZINC | 0.778 | 259.2 Da LogP 3.09 TPSA 89.7 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(Oc2ccc([N+](=O)[O-])cc2)cc1
|
| ZINC2504355 ZINC | 0.778 | 226.2 Da LogP 2.62 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(C(=O)c2ccccc2)cc1
|
| ZINC16892582 ZINC | 0.769 | 214.2 Da LogP 0.35 TPSA 106.7 | ✓ Ro5 | ✓ Clean |
NC(=S)N/N=C\c1ccc([N+](=O)[O-])o1
|
| ZINC967470 ZINC | 0.769 | 214.2 Da LogP 0.35 TPSA 106.7 | ✓ Ro5 | ✓ Clean |
NC(=S)N/N=C/c1ccc([N+](=O)[O-])o1
|
| ZINC1592410 ZINC | 0.739 | 212.2 Da LogP 1.54 TPSA 59.9 | ✓ Ro5 | Alert |
O=C(C(=O)c1cccnc1)c1cccnc1
|
| ZINC2173334 ZINC | 0.739 | 300.2 Da LogP 2.57 TPSA 120.4 | ✓ Ro5 | Alert |
O=C(C(=O)c1ccc([N+](=O)[O-])cc1)c1ccc([N+](=O)[…
|
| ZINC4892440 ZINC | 0.724 | 301.3 Da LogP 2.94 TPSA 121.6 | ✓ Ro5 | ✓ Clean |
O=C(Nc1ccc(C(=O)O)cc1)Nc1ccc([N+](=O)[O-])cc1
|
| ZINC1556486 ZINC | 0.720 | 266.3 Da LogP 3.39 TPSA 57.5 | ✓ Ro5 | ✓ Clean |
O=C(/C=C/c1ccccc1O)/C=C/c1ccccc1O
|
| ZINC1688116 ZINC | 0.708 | 272.2 Da LogP 2.73 TPSA 103.3 | ✓ Ro5 | ✓ Clean |
O=C(c1ccc([N+](=O)[O-])cc1)c1ccc([N+](=O)[O-])c…
|
| ZINC1857777485 ZINC | 0.704 | 224.3 Da LogP 3.29 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
O=C(C=Cc1ccccc1O)c1ccccc1
|
| ZINC3894725 ZINC | 0.704 | 224.3 Da LogP 3.29 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
O=C(/C=C/c1ccccc1O)c1ccccc1
|
| ZINC4566597 ZINC | 0.704 | 224.3 Da LogP 3.29 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
O=C(/C=C\c1ccccc1O)c1ccccc1
|
| ZINC123863 ZINC | 0.700 | 286.2 Da LogP 2.55 TPSA 109.5 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(NC(=O)c2ccc([N+](=O)[O-])cc2)cc1
|
| ZINC1532902 ZINC | 0.700 | 206.2 Da LogP -0.86 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O
|
| ZINC15636539 ZINC | 0.700 | 287.2 Da LogP 2.51 TPSA 106.7 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(OC(=O)c2ccc([N+](=O)[O-])cc2)cc1
|
| ZINC2018106 ZINC | 0.700 | 206.2 Da LogP -0.86 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
O=C(O)CC[C@](O)(CC(=O)O)C(=O)O
|
| ZINC3129761 ZINC | 0.700 | 383.4 Da LogP 3.79 TPSA 114.6 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(S(=O)(=O)c2ccc(-c3ccc([N+](=O)[O-])…
|
| ZINC12359024 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)C(=O)O
|
| ZINC13533920 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O
|
| ZINC1532740 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)C(=O)O
|
| ZINC1549593 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O
|
| ZINC2013424 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)C(=O)O
|
| ZINC2555760 ZINC | 0.692 | 255.2 Da LogP 2.66 TPSA 77.3 | ✓ Ro5 | Alert |
O=C(C(=O)c1ccc([N+](=O)[O-])cc1)c1ccccc1
|
| ZINC3581021 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O
|
| ZINC3860635 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)C(=O)O
|
| ZINC5783661 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(=O)O
|
| ZINC6072527 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O
|
| ZINC1672966 ZINC | 0.688 | 210.2 Da LogP 2.75 TPSA 34.1 | ✓ Ro5 | Alert |
O=C(C(=O)c1ccccc1)c1ccccc1
|
| ZINC34057267 ZINC | 0.684 | 274.3 Da LogP 4.72 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(-c2ccc(-c3ccccc3)cc2)cc1
|
| ZINC1556187 ZINC | 0.679 | 316.2 Da LogP 2.43 TPSA 140.7 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(C(=O)c2cc([N+](=O)[O-])cc([N+](=O)[…
|
| ZINC12360002 ZINC | 0.671 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…
|
| ZINC12503599 ZINC | 0.671 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…
|
| ZINC16546165 ZINC | 0.671 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…
|
| ZINC31977053 ZINC | 0.671 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…
|
| ZINC4806433 ZINC | 0.671 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…
|
| ZINC53683898 ZINC | 0.671 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…
|
| ZINC8586019 ZINC | 0.671 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…
|
| ZINC8586020 ZINC | 0.671 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…
|
| ZINC8586021 ZINC | 0.671 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…
|
| ZINC8586022 ZINC | 0.671 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…
|
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.