KpKP13 Protein target profile

Fumarate nitrate reduction regulatory protein

Accession: KP13_05031

Gene: AHE44794.1 fnr 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GMU3
Length 250
Pocket druggability (P2Rank · AlphaFold DB model) 0.882
Direct ligand evidence 0 56 total records
Functional annotation 0 EC 8 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
3.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
90.06 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

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) 0.882
Structure A0A0H3GMU3
Pocket Pocket 1
Druggability (FPocket) 0.511
Structure A0A0H3GMU3
Pocket Pocket 1
ColabFold model
P2Rank 0.845 · Pocket 1
FPocket 0.235 · Pocket 14
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 146 / 4744 genomes with a hit
Prevalence 3.1%

Sequence

Primary amino-acid sequence viewer.

MIPEKRIIRRIQSGGCAIHCQDCSISQLCIPFTLNEHELDQLDNIIERKKPIQKGQTLFKAGDELKSLYAIRSGTIKSYTITEQGDEQITGFHLAGDLVGFDAIGTGLHPSFAQALETSMVCEIPFETLDDLSGKMPNLRQQMMRLMSGEIKGDQDMILLLSKKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQKSGMLAVKGKYITIENSDLLAQLAGQARNVA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

8
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0032993 A macromolecular complex containing both protein and DNA molecules.
  • 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:0001216 A DNA-binding transcription factor activity that activates or increases transcription of specific gene sets.
  • GO:0000976 Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
34 144 CDD cd00038 CAP_ED
34 144 InterPro IPR000595 Cyclic nucleotide-binding domain
51 132 Pfam PF00027 Cyclic nucleotide-binding domain
51 132 InterPro IPR000595 Cyclic nucleotide-binding domain
209 224 PRINTS PR00034 CRP bacterial regulatory protein HTH signature
209 224 InterPro IPR012318 Crp-type HTH domain
193 209 PRINTS PR00034 CRP bacterial regulatory protein HTH signature
193 209 InterPro IPR012318 Crp-type HTH domain
165 250 Gene3D G3DSA:1.10.10.10 -
165 250 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
30 151 SMART SM00100 cnmp_10
30 151 InterPro IPR000595 Cyclic nucleotide-binding domain
50 244 PANTHER PTHR24567 CRP FAMILY TRANSCRIPTIONAL REGULATORY PROTEIN
187 235 SMART SM00419 crpmeuga4
187 235 InterPro IPR012318 Crp-type HTH domain
193 224 Pfam PF00325 Bacterial regulatory proteins, crp family
193 224 InterPro IPR012318 Crp-type HTH domain
23 162 SUPERFAMILY SSF51206 cAMP-binding domain-like
23 162 InterPro IPR018490 Cyclic nucleotide-binding domain superfamily
30 104 ProSiteProfiles PS50042 cAMP/cGMP binding motif profile.
30 104 InterPro IPR000595 Cyclic nucleotide-binding domain
195 218 ProSitePatterns PS00042 Crp-type HTH domain signature.
195 218 InterPro IPR018335 Transcription regulator HTH, Crp-type, conserved site
19 164 Gene3D G3DSA:2.60.120.10 Jelly Rolls
19 164 InterPro IPR014710 RmlC-like jelly roll fold
166 233 CDD cd00092 HTH_CRP
19 164 FunFam G3DSA:2.60.120.10:FF:000004 Fumarate/nitrate reduction transcriptional regulator Fnr
164 237 ProSiteProfiles PS51063 Crp-type HTH domain profile.
164 237 InterPro IPR012318 Crp-type HTH domain
165 245 FunFam G3DSA:1.10.10.10:FF:000028 Fumarate/nitrate reduction transcriptional regulator Fnr
165 244 SUPERFAMILY SSF46785 Winged helix DNA-binding domain
165 244 InterPro IPR036390 Winged helix DNA-binding domain superfamily

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 · P2Rank

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

Pocket 1 P2Rank #1
0.882
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.22
Likely same site as FPocket 9 2.0 Å 11 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.095
Likely same site as FPocket 1 2.1 Å 9 shared residues 100% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.012
Likely same site as FPocket 11 2.7 Å 7 shared residues 100% of smaller site
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.511
Likely same site as P2Rank 3 2.1 Å 9 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #9
0.361
Likely same site as P2Rank 2 2.0 Å 11 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 3 FPocket #11
0.356
Likely same site as P2Rank 4 2.7 Å 7 shared residues 100% of smaller site
Show in viewer
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_A0A0H3GMU3
AlphaFold DB full sequence Viewing
ColabFold KP13_05031
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.

56 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 6 records from similar proteins
Structural ligands 6 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2FT PDB via homolog 168.1 Da · LogP 0.57 · TPSA 74.6 Open detail RCSB PDB
AKG PDB via homolog Detail RCSB PDB
BTB PDB via homolog Detail RCSB PDB
FES PDB via homolog Detail RCSB PDB
PCG 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
2FT RCSB PDB P0A4U6 168.1 Da LogP 0.57 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(C(=O)O)(F)F)C(=O)O
AKG RCSB PDB P0A4U6 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
BTB RCSB PDB P29283 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
FES RCSB PDB Q70ET4 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
PCG RCSB PDB C3SQJ7 345.2 Da LogP -1.52 TPSA 174.8 ✓ Ro5 ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@H]4C(O3)CO[P@](=O)(O4)…
SP1 RCSB PDB P0ACJ8 345.3 Da LogP -0.70 TPSA 137.8 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)C…

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.