Protein target profile

VK055_2586

nicotinamide-nucleotide adenylyltransferase

Genome: KpATCC43816 Gene: AIK81183.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GM95
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Length 410
Pocket druggability 0.958
Metabolic reactions 1
Chokepoint No
Functional annotation 2 EC 9 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.

Main supporting evidence

No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.94. Review the complete evidence below

Risks to review

Microbiome similarity 128 of 4744 screened genomes (2.7%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.96) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.96, but this pocket's geometry is unusually large/diffuse compared to this protein's other predicted pockets — may reflect a low-confidence or disordered model region rather than a real cavity.

Evidence gaps

No ligand evidence No experimental PDB ligands, measured ChEMBL bioactivity, or proposed ZINC compound records are available.
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
2.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
54.441 Higher values support similarity to known essential genes.
DEG E-value
9.78e-141 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
91.39 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

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 0.958
Structure A0A0H3GM95
Pocket Pocket 2
P2Rank 0.942
Structure A0A0H3GM95
Pocket Pocket 1
ColabFold model
FPocket 0.872 · Pocket 3
P2Rank 0.943 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 128 / 4744 genomes with a hit
Prevalence 2.7%

Cross-references

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

Sequence

UniProt A0A0H3GM95

Pathways

KEGG R00137 BioCyc 2.7.7.1-RXN

Metabolic context

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

Explore metabolic network

Metabolic context: no human homolog detected.

Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Pathways
Nicotinate and nicotinamide metabolism
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.

MSSFDYLKSAIKQKGCTLQQVAEASGMTKGYLSQLLNAKIKSPSAQKLEALHRFLGLEFPRRQKSVGVVFGKFYPLHTGHIYLIQRACSQVDELHIIMGYDDTRDRELFEESAMSQQPTVPDRLRWLLQTFKYQKNIRIHAFNEEGMEPYPHGWDVWSHGIRAFMSEKGIEPNRIYTSEEADAPQYLEHLGIETVLIDPKRTFMNISGGQIRENPFRYWEYIPTEVKPFFVRTVAILGGESSGKSTLVNKLANIFNTTSAWEYGRDYVFSHLGGDEMALQYSDYDKIALGHAQYIDFAVKYANKVAFIDTDFVSTQAFCLKYEGREHPFVQALIDEYRFDLVILLENNTPWVADGLRSLGSSVDRKEFQSLLVSLLKENEIEFVHVKESDYDARFLRCVELVKQLMGEQG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 9 GO

Enzyme Commission (EC)

2

Gene Ontology (GO)

9
  • GO:0050262 Catalysis of the reaction: beta-nicotinamide D-riboside + ATP = beta-nicotinamide D-ribonucleotide + ADP + H+.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0009435 The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD+), a coenzyme that interconverts with its reduced form, NADH, in many redox and catabolic reactions. NAD+ is derived from various sources including vitamin B3.
  • GO:0000309 Catalysis of the reaction: beta-nicotinamide D-ribonucleotide + ATP + H+ = diphosphate + NAD+.
  • GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

34 records
Show feature table
Start End DB Term Name
232 386 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
232 386 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
64 395 NCBIfam TIGR01526 nicotinamide-nucleotide adenylyltransferase
64 395 InterPro IPR006417 Nicotinamide-nucleotide adenylyltransferase
66 136 NCBIfam TIGR00125 cytidyltransferase-like domain
66 136 InterPro IPR004821 Cytidyltransferase-like domain
66 227 CDD cd02167 NMNAT_NadR
66 227 InterPro IPR041749 NadR, nicotinamide/nicotinate mononucleotide adenylyltransferase domain
5 60 FunFam G3DSA:1.10.260.40:FF:000020 Trifunctional nicotinamide-nucleotide adenylyltransferase/ribosylnicotinamide kinase/transcriptional regulator NadR
231 397 Gene3D G3DSA:3.40.50.300 -
231 397 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
2 410 PIRSF PIRSF004776 NadR_NMNAT/RNK
2 410 InterPro IPR016429 NAD biosynthesis/regulator protein NadR
6 60 SUPERFAMILY SSF47413 lambda repressor-like DNA-binding domains
6 60 InterPro IPR010982 Lambda repressor-like, DNA-binding domain superfamily
5 60 Gene3D G3DSA:1.10.260.40 -
5 60 InterPro IPR010982 Lambda repressor-like, DNA-binding domain superfamily
7 58 Pfam PF01381 Helix-turn-helix
7 58 InterPro IPR001387 Cro/C1-type helix-turn-helix domain
233 260 CDD cd02019 NK
66 229 SUPERFAMILY SSF52374 Nucleotidylyl transferase
63 230 Gene3D G3DSA:3.40.50.620 HUPs
63 230 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
63 230 FunFam G3DSA:3.40.50.620:FF:000091 Trifunctional nicotinamide-nucleotide adenylyltransferase/ribosylnicotinamide kinase/transcriptional regulator NadR
231 397 FunFam G3DSA:3.40.50.300:FF:000672 Trifunctional nicotinamide-nucleotide adenylyltransferase/ribosylnicotinamide kinase/transcriptional regulator NadR
7 59 CDD cd00093 HTH_XRE
7 59 InterPro IPR001387 Cro/C1-type helix-turn-helix domain
7 62 ProSiteProfiles PS50943 Cro/C1-type HTH domain profile.
7 62 InterPro IPR001387 Cro/C1-type helix-turn-helix domain
6 62 SMART SM00530 mbf_short4
6 62 InterPro IPR001387 Cro/C1-type helix-turn-helix domain
234 394 Pfam PF13521 AAA domain
234 394 InterPro IPR038727 NadR/Ttd14, AAA domain
66 409 PANTHER PTHR37512 TRIFUNCTIONAL NAD BIOSYNTHESIS/REGULATOR PROTEIN NADR

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 · FPocket

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

Site 1 FPocket #2
0.958
Likely same site as P2Rank 1 1.9 Å 34 shared residues 94% of smaller site
Unusual size
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Surrounding area
Site 2 FPocket #17
0.816
Likely same site as P2Rank 2 1.2 Å 14 shared residues 100% of smaller site
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Surrounding area
Site 3 FPocket #7
0.261
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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.942
Likely same site as FPocket 2 1.9 Å 34 shared residues 94% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.629
Likely same site as FPocket 17 1.2 Å 14 shared residues 100% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.289
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Surrounding area
Site 4 P2Rank #4
0.044
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Surrounding area
Site 5 P2Rank #5
0.027
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Surrounding area
Residue sets
UniProt: Binding site:104-104
UniProt: Binding site:144-157
UniProt: Binding site:177-179
UniProt: Binding site:204-206
UniProt: Binding site:259-261
UniProt: Binding site:70-73
UniProt: Binding site:77-77
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_A0A0H3GM95
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_2586
ColabFold — — full sequence — Loaded