Protein target profile

VK055_2370

lipid-A-disaccharide synthase

Genome: KpATCC43816 Gene: lpxB AIK80967.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 6 reactions UniProt A0A0H3GNK2
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Length 383
Pocket druggability 0.92
Metabolic reactions 6
Chokepoint Yes
Functional annotation 1 EC 4 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Metabolic bottleneck Catalyzes a reaction that is the only producer or consumer of a metabolite in the imported metabolic model. Central metabolic position More central than 93.7% of genes in this genome. 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. Review the complete evidence below

Risks to review

Microbiome similarity 162 of 4744 screened genomes (3.4%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.92) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.92, 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. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.36.

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
3.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
94.58 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 0.92
Structure A0A0H3GNK2
Pocket Pocket 4
P2Rank 0.359
Structure A0A0H3GNK2
Pocket Pocket 1
ColabFold model
FPocket 0.175 · Pocket 19
P2Rank 0.468 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 162 / 4744 genomes with a hit
Prevalence 3.4%

Cross-references

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

Sequence

UniProt A0A0H3GNK2

Pathways

BioCyc RXN-23219 BioCyc RXN-22237 BioCyc RXN2DNV-2 BioCyc RXN2B4Q-52 KEGG R04606 BioCyc LIPIDADISACCHARIDESYNTH-RXN BioCyc RXN-20785

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a producing & consuming chokepoint reaction in Lipopolysaccharide biosynthesis, no isoenzyme backup detected, more central than 93.7% of genes in this genome, no human homolog detected.

Relative network centrality 93.7% more central than 93.7% of genes in this genome
Chokepoint Chokepoint gene
Pathways
Lipopolysaccharide biosynthesis
Catalyzed reactions

6 reactions 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.

MAEQRPLTIALVAGETSGDILGAGLIRALKARIPNARFVGVAGPLMQAEGCEAWYEMEELAVMGIVEVLGRLRRLLHIRADLTRRFGELRPDVFVGIDAPDFNITLEGNLKKQGIKTIHYVSPSVWAWRQKRVFKIGRSTDLVLAFLPFEKAFYDKFNVPCRFIGHTMADAMPLDPDKGAARDRLGIPHSVRCLALLPGSRGAEVEMLSADFLKTAQLLRATYPDLQVVVPLVNAKRREQFERIKAETAPDMIVHMLDGQARDAMIASDAALLASGTAALECMLAKCPMVVGYRMKPFTFWLAKRLVKTDYVSLPNLLAGRELVKELLQDECEPQALAAALQPLLADGKTSHEMHETFRALHQQIRCNADEQAADAVLELAKQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0009245 The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
  • GO:0008915 Catalysis of the reaction: a lipid X + a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-alpha-D-glucosamine = a lipid A disaccharide + UDP + H+.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0005543 Binding to a phospholipid, a class of lipids containing phosphoric acid as a mono- or diester.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

10 records
Show feature table
Start End DB Term Name
2 383 PANTHER PTHR30372 LIPID-A-DISACCHARIDE SYNTHASE
2 383 InterPro IPR003835 Glycosyl transferase, family 19
1 380 NCBIfam TIGR00215 lipid-A-disaccharide synthase
1 380 InterPro IPR003835 Glycosyl transferase, family 19
9 378 SUPERFAMILY SSF53756 UDP-Glycosyltransferase/glycogen phosphorylase
9 377 Pfam PF02684 Lipid-A-disaccharide synthetase
9 377 InterPro IPR003835 Glycosyl transferase, family 19
36 293 CDD cd01635 Glycosyltransferase_GTB-type
6 382 Hamap MF_00392 Lipid-A-disaccharide synthase [lpxB].
6 382 InterPro IPR003835 Glycosyl transferase, family 19

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 #4
0.92
Unusual size
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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
0.359
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Surrounding area
Site 2 P2Rank #2
0.262
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Surrounding area
Site 3 P2Rank #3
0.248
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Surrounding area
Site 4 P2Rank #4
0.078
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Surrounding area
Site 5 P2Rank #5
0.066
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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_A0A0H3GNK2
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_2370
ColabFold — — full sequence — Loaded