KpATCC43816 Protein target profile

nadE

Accession: VK055_1230

Gene: AIK79853.1 nadE 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GVX9
Length 275
Pocket druggability (P2Rank · AlphaFold DB model) 0.935
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 55 total records
Functional annotation 1 EC 7 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
7.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
90.182 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
96.48 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) 0.935
Structure A0A0H3GVX9
Pocket Pocket 1
Druggability (FPocket) 0.685
Structure A0A0H3GVX9
Pocket Pocket 12
ColabFold model
P2Rank 0.965 · Pocket 1
FPocket 0.529 · Pocket 12
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 341 / 4744 genomes with a hit
Prevalence 7.2%

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
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.

MTLQQEIIQALGAKPQIDVAGEIRRSVDFLKSYLQTYPFIKSLVLGISGGQDSTLTGKLCQIAINELRAETGDSSLQFIAVRLPYGVQADEQDCQDAIAFIQPDRVLTVNIKAAVLASEQALREAGIELSDFVRGNEKARERMKAQYSIAGMTKGVVVGTDHAAEAITGFFTKYGDGGTDINPIFRLNKRQGKQLLAHLGCPEHLYKKLPTADLEDDRPSLPDEVALGVTYENIDDYLEGKTLDPSIAKTIEGWYLKTEHKRRPPITVFDDFWKK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • 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:0004359 Catalysis of the reaction: L-glutamine + H2O = L-glutamate + NH4+.
  • GO:0008795 Catalysis of the reaction: deamido-NAD+ + NH4+ + ATP = AMP + diphosphate + NAD+ + H+.
  • GO:0003952 Catalysis of the reaction: deamido-NAD+ + L-glutamine + ATP + H2O = L-glutamate + AMP + diphosphate + NAD+ + H+.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
17 262 CDD cd00553 NAD_synthase
17 262 InterPro IPR003694 NAD(+) synthetase
1 275 Gene3D G3DSA:3.40.50.620 HUPs
1 275 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
1 274 FunFam G3DSA:3.40.50.620:FF:000015 NH(3)-dependent NAD(+) synthetase
23 265 Pfam PF02540 NAD synthase
23 265 InterPro IPR022310 NAD/GMP synthase
3 273 SUPERFAMILY SSF52402 Adenine nucleotide alpha hydrolases-like
25 239 PANTHER PTHR23090 NH 3 /GLUTAMINE-DEPENDENT NAD + SYNTHETASE
25 239 InterPro IPR003694 NAD(+) synthetase
18 275 NCBIfam TIGR00552 NAD(+) synthase
18 275 InterPro IPR003694 NAD(+) synthetase
18 268 Hamap MF_00193 NH(3)-dependent NAD(+) synthetase [nadE].
18 268 InterPro IPR022926 NH(3)-dependent NAD(+) synthetase

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

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
0.935
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.642
Likely same site as FPocket 12 1.0 Å 20 shared residues 95% of smaller site
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.089
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #12
0.685
Likely same site as P2Rank 2 1.0 Å 20 shared residues 95% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:140-140 in other chain
UniProt: Binding site:160-160
UniProt: Binding site:165-165
UniProt: Binding site:173-173 in other chain
UniProt: Binding site:180-180
UniProt: Binding site:189-189
UniProt: Binding site:211-211
UniProt: Binding site:260-261 in other chain
UniProt: Binding site:46-53
UniProt: Binding site:52-52
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_A0A0H3GVX9
AlphaFold DB full sequence Viewing
ColabFold VK055_1230
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.

55 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ADJ PDB via homolog 999.7 Da · LogP -4.15 · TPSA 469.8 Open detail RCSB PDB
APC PDB via homolog Detail RCSB PDB
DND PDB via homolog Detail RCSB PDB
DPO PDB via homolog Detail RCSB PDB
POP 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
ADJ RCSB PDB P08164 999.7 Da LogP -4.15 TPSA 469.8 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
APC RCSB PDB P08164 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
DND RCSB PDB P18843 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(…
DPO RCSB PDB P18843 173.9 Da LogP -3.34 TPSA 135.6 ✓ Ro5 ✓ Clean [O-]P(=O)([O-])OP(=O)([O-])[O-]
POP RCSB PDB P08164 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=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.

Cross-references

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