KpATCC43816 Protein target profile

ribulose-phosphate 3-epimerase

Accession: VK055_3713

Gene: AIK82268.1 rpe 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GYE8
Length 225
Pocket druggability (P2Rank · AlphaFold DB model) 0.819
Metabolic reactions 2
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
Hit
Human identity (%)
39.459 Lower values reduce human off-target concern.
Human E-value
1.84e-39
Gut microbiome similarity
13.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
94.643 Higher values support similarity to known essential genes.
DEG E-value
4.57e-158 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
97.41 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) 0.819
Structure A0A0H3GYE8
Pocket Pocket 1
Druggability (FPocket) 0.267
Structure A0A0H3GYE8
Pocket Pocket 3
ColabFold model
P2Rank 0.865 · Pocket 1
FPocket 0.208 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 661 / 4744 genomes with a hit
Prevalence 13.9%

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 95.5% of genes in this genome.

Relative network centrality 95.5% more central than 95.5% of genes in this genome
Chokepoint Not a chokepoint
Catalyzed reactions

2 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.

MKQYLIAPSILSADFARLGEDTAKALAAGADVVHFDVMDNHYVPNLTIGPMVLKSLRNYGITAPIDVHLMVKPVDRIIPDFAEAGASIITFHPEASEHVDRSLQLIKEHGCKAGLVFNPATPLSYLDYVMDKLDVILLMSVNPGFGGQSFIPQTLDKLREVRQRIDASGYDIRLEVDGGVKASNIGEIAAAGADMFVAGSAIFGQPDYKQVIDQMRSELAKVSHG

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:0016857 Catalysis of a reaction that alters the configuration of one or more chiral centers in a carbohydrate molecule.
  • GO:0004750 Catalysis of the reaction: D-ribulose 5-phosphate = D-xylulose 5-phosphate.
  • GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
  • GO:0006098 The metabolic process in which glucose-6-phosphate is oxidized to form carbon dioxide (CO2) and ribulose 5-phosphate, coupled to reduction of NADP+ to NADPH; ribulose 5-P then enters a series of reactions that can yield biosynthetic precursors (ribose-5-phosphate and erythrose-4-phosphate) and glycolytic intermediates (fructose-6-phosphate and glyceraldehyde-3-phosphate).
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0046872 Binding to a metal ion.
  • GO:0019323 The chemical reactions and pathways resulting in the breakdown of a pentose, any monosaccharide with a chain of five carbon atoms in the molecule.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
5 216 CDD cd00429 RPE
5 216 InterPro IPR000056 Ribulose-phosphate 3-epimerase-like
1 223 Gene3D G3DSA:3.20.20.70 Aldolase class I
1 223 InterPro IPR013785 Aldolase-type TIM barrel
33 47 ProSitePatterns PS01085 Ribulose-phosphate 3-epimerase family signature 1.
33 47 InterPro IPR000056 Ribulose-phosphate 3-epimerase-like
1 225 PIRSF PIRSF001461 RPE
1 225 InterPro IPR026019 Ribulose-phosphate 3-epimerase
3 218 SUPERFAMILY SSF51366 Ribulose-phoshate binding barrel
3 218 InterPro IPR011060 Ribulose-phosphate binding barrel
136 158 ProSitePatterns PS01086 Ribulose-phosphate 3-epimerase family signature 2.
136 158 InterPro IPR000056 Ribulose-phosphate 3-epimerase-like
6 203 Pfam PF00834 Ribulose-phosphate 3 epimerase family
6 203 InterPro IPR000056 Ribulose-phosphate 3-epimerase-like
5 216 NCBIfam TIGR01163 ribulose-phosphate 3-epimerase
5 216 InterPro IPR026019 Ribulose-phosphate 3-epimerase
1 222 FunFam G3DSA:3.20.20.70:FF:000004 Ribulose-phosphate 3-epimerase
5 221 PANTHER PTHR11749 RIBULOSE-5-PHOSPHATE-3-EPIMERASE
5 221 InterPro IPR000056 Ribulose-phosphate 3-epimerase-like
3 218 Hamap MF_02227 Ribulose-phosphate 3-epimerase [rpe].
3 218 InterPro IPR026019 Ribulose-phosphate 3-epimerase

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
0.819
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Surrounding area
Pocket 2 P2Rank #2
0.038
Likely same site as FPocket 3 1.6 Å 11 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.011
Likely same site as FPocket 2 2.9 Å 8 shared residues 100% of smaller site
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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 #3
0.267
Likely same site as P2Rank 2 1.6 Å 11 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #2
0.209
Likely same site as P2Rank 3 2.9 Å 8 shared residues 100% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:177-177 Proton donor
UniProt: Active site:36-36 Proton acceptor
UniProt: Binding site:144-147
UniProt: Binding site:177-177
UniProt: Binding site:177-179
UniProt: Binding site:179-179
UniProt: Binding site:199-200
UniProt: Binding site:34-34
UniProt: Binding site:36-36
UniProt: Binding site:68-68
UniProt: Binding site:9-9
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_A0A0H3GYE8
AlphaFold DB full sequence Viewing
ColabFold VK055_3713
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
5RP PDB via homolog 230.1 Da · LogP -2.62 · TPSA 144.5 Open detail RCSB PDB
5SP PDB via homolog Detail RCSB PDB
DX5 PDB via homolog Detail RCSB PDB
S6P PDB via homolog Detail RCSB PDB
XPE 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
5RP RCSB PDB Q96AT9 230.1 Da LogP -2.62 TPSA 144.5 ✓ Ro5 ✓ Clean C([C@H]([C@H](C(=O)CO)O)O)OP(=O)(O)O
5SP RCSB PDB Q96AT9 230.1 Da LogP -2.62 TPSA 144.5 ✓ Ro5 ✓ Clean C([C@H]([C@@H](C(=O)CO)O)O)OP(=O)(O)O
DX5 RCSB PDB Q9A1H8 232.1 Da LogP -2.83 TPSA 147.7 1 viol. ✓ Clean C([C@@H]([C@H]([C@@H](COP(=O)(O)O)O)O)O)O
S6P RCSB PDB P32719 262.2 Da LogP -3.47 TPSA 167.9 1 viol. ✓ Clean C([C@@H]([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)…
XPE RCSB PDB Q96AT9 458.5 Da LogP -0.88 TPSA 123.5 1 viol. ✓ Clean C(COCCOCCOCCOCCOCCOCCOCCOCCOCCO)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.