Genome KpKP13

Protein target profile

ADP-heptose--LPS heptosyltransferase 2

Accession: KP13_00201

Gene: rfaF AHE42115.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H038
Length 342
Pocket druggability (P2Rank) 0.861
Direct ligand evidence 0 51 total records
Functional annotation 1 EC 5 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
3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
91.66 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) 0.861
Structure A0A0H3H038
Pocket Pocket 1
Druggability (FPocket) 0.05
Structure A0A0H3H038
Pocket Pocket 25
ColabFold model
P2Rank 0.828 · Pocket 1
FPocket 0.366 · Pocket 28
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 144 / 4744 genomes with a hit
Prevalence 3.0%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MGDMMMSQSLYRTLRARYPQAIIDVMAPAWCRPLLSRMPEVNEAIPMPLGHGALAIGERRKLGHSLRERRYDRAYVLPNSFKSALVPFFANIPLRTGWRGEMRYGLLNDARVLDKDAWPLMVERYVALAYDNGVMRCAKDLPQPLLWPQLQVNEGEKSQACSAFNLSNDRPIVGFCPGAEFGPAKRWPHYHYAALAKKLIDDGYQIALFGSAKDNEAGKEIIAALSSEQQAWCRNLAGETQLEQAVILIAACKAVVTNDSGLMHVAAALDRPLVALYGPSSPDFTPPLSHKARVIRLITGYHKVRKGDAAEGYHQSLIDITPERVLQELNELLAEKTEHEEA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0009103 The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
  • GO:0016757 Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0008713 Catalysis of the reaction: heptosyl-KDO2-lipid A + ADP-L-glycero-beta-D-manno-heptose = heptosyl2-KDO2-lipid A + ADP + H+.
  • GO:0009244 The chemical reactions and pathways resulting in the formation of the core region of bacterial lipopolysaccharides, which contains ten saccharide residues.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
153 337 Gene3D G3DSA:3.40.50.2000 Glycogen Phosphorylase B;
155 334 FunFam G3DSA:3.40.50.2000:FF:000023 ADP-heptose--LPS heptosyltransferase II
59 314 Pfam PF01075 Glycosyltransferase family 9 (heptosyltransferase)
59 314 InterPro IPR002201 Glycosyl transferase, family 9
1 141 Gene3D G3DSA:3.40.50.2000 Glycogen Phosphorylase B;
1 140 FunFam G3DSA:3.40.50.2000:FF:000022 ADP-heptose--LPS heptosyltransferase II
1 337 PANTHER PTHR30160 TETRAACYLDISACCHARIDE 4'-KINASE-RELATED
1 335 SUPERFAMILY SSF53756 UDP-Glycosyltransferase/glycogen phosphorylase
1 333 NCBIfam TIGR02195 lipopolysaccharide heptosyltransferase II
1 333 InterPro IPR011910 ADP-heptose--LPS heptosyltransferase 2
1 331 CDD cd03789 GT9_LPS_heptosyltransferase
1 331 InterPro IPR002201 Glycosyl transferase, family 9

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

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

Pocket 1 P2Rank #1
0.861
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Surrounding area
Pocket 2 P2Rank #2
0.476
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Surrounding area
Pocket 3 P2Rank #3
0.469
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Surrounding area
Pocket 4 P2Rank #4
0.071
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Surrounding area
Pocket 5 P2Rank #5
0.016
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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_A0A0H3H038
AlphaFold DB full sequence Viewing
ColabFold KP13_00201
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.

51 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 1 records from similar proteins
Structural ligands 1 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
AFH PDB via homolog 621.4 Da · LogP -3.58 · TPSA 311.7 Open detail RCSB PDB
ZINC12360002 ZINC proposed compound · Tanimoto 0.671 Detail ZINC
ZINC12360703 ZINC proposed compound · Tanimoto 0.671 Detail ZINC
ZINC12503599 ZINC proposed compound · Tanimoto 0.671 Detail ZINC
ZINC16546165 ZINC proposed compound · Tanimoto 0.671 Detail ZINC

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
AFH RCSB PDB P24173 621.4 Da LogP -3.58 TPSA 311.7 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.