KpATCC43816 Protein target profile

L-ribulose-5-phosphate 4-epimerase

Accession: VK055_2514

Gene: araD AIK81111.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GMG9
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Length 231
Pocket druggability (P2Rank · AlphaFold DB model) 0.583
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 2 total records
Functional annotation 1 EC 6 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

Central metabolic position More central than 98.5% of genes in this genome. 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. Moderate predicted binding pocket FPocket selected-pocket score 0.41. This supports review but is not experimental validation. Review the complete evidence below

Risks to review

Microbiome similarity 1225 of 4744 screened genomes (25.8%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.58) — check the ligand evidence before deprioritizing on off-target risk alone.

Evidence coverage

Core evidence streams are available for this target.
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
25.8% 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
96.71 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) 0.583
Structure A0A0H3GMG9
Pocket Pocket 1
Druggability (FPocket) 0.405
Structure A0A0H3GMG9
Pocket Pocket 4
ColabFold model
P2Rank 0.498 · Pocket 1
FPocket 0.451 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 1225 / 4744 genomes with a hit
Prevalence 25.8%

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 98.5% of genes in this genome, no human homolog detected.

Relative network centrality 98.5% more central than 98.5% of genes in this genome
Chokepoint Not a chokepoint
Pathways
Ascorbate and aldarate metabolism Pentose and glucuronate interconversions
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.

MLEDLKRQVLEANLALPKHNLVTLTWGNVSAVDREKGVFVIKPSGVDYRVMTADDMVVVSLESGEVVEGNKKPSSDTPTHRLLYQAFPTLGGIVHTHSRHATIWAQAGQSIPATGTTHADYFYGPVPCTRLMTDAEINGDYEWETGNVIVETFRQQGIDPAQMPGVLVHSHGPFAWGKNAEDAVHNAIVLEEIAYMGIFCRQLAPQLPAMQQTLLDKHYLRKHGAKAYYGQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0008270 Binding to a zinc ion (Zn).
  • GO:0008742 Catalysis of the reaction: L-ribulose 5-phosphate = D-xylulose 5-phosphate.
  • GO:0019569 The chemical reactions and pathways resulting in the breakdown of L-arabinose into D-xylulose 5-phosphate.
  • GO:0019572 The chemical reactions and pathways resulting in the breakdown of L-arabinose, the L-enantiomer of arabino-pentose.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0016832 Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
2 230 PANTHER PTHR22789 FUCULOSE PHOSPHATE ALDOLASE
8 195 Pfam PF00596 Class II Aldolase and Adducin N-terminal domain
8 195 InterPro IPR001303 Class II aldolase/adducin N-terminal
3 223 CDD cd00398 Aldolase_II
1 231 Hamap MF_00989 L-ribulose-5-phosphate 4-epimerase [araD].
1 231 InterPro IPR033748 L-ribulose-5-phosphate 4-epimerase AraD
7 198 SMART SM01007 Aldolase_II_2
7 198 InterPro IPR001303 Class II aldolase/adducin N-terminal
1 231 FunFam G3DSA:3.40.225.10:FF:000001 L-ribulose-5-phosphate 4-epimerase UlaF
1 231 Gene3D G3DSA:3.40.225.10 -
1 231 InterPro IPR036409 Class II aldolase/adducin N-terminal domain superfamily
1 231 NCBIfam TIGR00760 L-ribulose-5-phosphate 4-epimerase
1 231 InterPro IPR004661 L-ribulose-5-phosphate 4-epimerase
1 223 SUPERFAMILY SSF53639 AraD/HMP-PK domain-like
1 223 InterPro IPR036409 Class II aldolase/adducin N-terminal 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
0.583
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Surrounding area
Pocket 2 P2Rank #2
0.482
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Surrounding area
Pocket 3 P2Rank #3
0.083
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Surrounding area
Pocket 4 P2Rank #4
0.064
Likely same site as FPocket 4 5.9 Å 7 shared residues 88% of smaller site
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Surrounding area
Pocket 5 P2Rank #5
0.024
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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 #4
0.405
Likely same site as P2Rank 4 5.9 Å 7 shared residues 88% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:120-120 Proton donor/acceptor
UniProt: Active site:229-229 Proton donor/acceptor
UniProt: Binding site:171-171
UniProt: Binding site:27-28
UniProt: Binding site:44-45
UniProt: Binding site:74-75
UniProt: Binding site:76-76
UniProt: Binding site:95-95
UniProt: Binding site:97-97
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_A0A0H3GMG9
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_2514
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.

2 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 2 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 0 similarity-based ZINC candidates
Best available ligand signal
13P PDB via homolog 170.1 Da · LogP -1.34 · TPSA 104.1 Open detail RCSB PDB
PGH 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
13P RCSB PDB
1E47
P0AB87 170.1 Da LogP -1.34 TPSA 104.1 ✓ Ro5 ✓ Clean C(C(=O)COP(=O)(O)O)O
PGH RCSB PDB
4FUA
P0AB87 171.0 Da LogP -1.40 TPSA 116.1 ✓ Ro5 ✓ Clean C(C(=O)NO)OP(=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.

Sequence

UniProt A0A0H3GMG9

Pathways

KEGG R05850 BioCyc RIBULPEPIM-RXN