Protein target profile

KP13_02836

glycerol dehydratase reactivase

Genome: KpKP13 Gene: AHE42595.1 3D evidence: Experimental + ColabFold model UniProt Q59474
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Length 607
Pocket druggability 0.938
Functional annotation 1 EC 3 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

Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.94, P2Rank 0.97). Use the 3D pocket comparison to verify whether they identify the same site. Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. 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. Review the complete evidence below

Risks to review

Microbiome similarity 161 of 4744 screened genomes (3.4%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.94) — check the ligand evidence before deprioritizing on off-target risk alone.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. 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)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
92.94 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.938
Structure 1NBW
Pocket Pocket 21
P2Rank 0.967
Structure 1NBW
Pocket Pocket 1
ColabFold model
FPocket 0.947 · Pocket 10
P2Rank 0.985 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 161 / 4744 genomes with a hit
Prevalence 3.4%

Cross-references

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

Sequence

UniProt Q59474

Structure

PDB 1NBW

Sequence

Primary amino-acid sequence viewer.

MPLIAGIDIGNATTEVALASDDPQARAFVASGIVATTGMKGTRDNIAGTLAALELALAKTPWSMSDVSRIYLNEAAPVIGDVAMETITETIITESTMIGHNPQTPGGVGVGVGTTIALGRLATLPAAQYAEGWIVLIDDAVDFLDAVWWLNEALDRGINVVAAILKKDDGVLVNNRLRKTLPVVDEVTLLEQVPEGVMAAVEVAAPGQVVRILSNPYGIATFFGLSPEETQAIVPIARALIGNRSAVVLKTPQGDVQSRVIPAGNLYISGEKRRGEADVAEGAEAIMQAMSACAPVRDIRGEPGTHAGGMLERVRKVMASLTGHEMSAIYIQDLLAVDTFIPRKVQGGMAGECAMENAVGMAAMVKADRLQMQVIARELSARLQTEVVVGGVEANMAIAGALTTPGCAAPLAILDLGAGSTDAAIVNAEGQITAVHLAGAGNMVSLLIKTELGLEDLSLAEAIKKYPLAKVESLFSIRHENGAVEFFREALSPAVFAKVVYIKEGELVPIDNASPLEKIRLVRRQAKEKVFVTNCLRALRQVSPGGSIRDIAFVVLVGGSSLDFEIPQLITEALSHYGVVAGQGNIRGTEGPRNAVATGLLLAGQAN

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

3
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0046405 Catalysis of the reaction: glycerol = 3-hydroxypropanal + H2O.
  • GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
92 256 Pfam PF18427 DD-reactivating factor swiveling domain
92 256 InterPro IPR040916 DD-reactivating factor swiveling domain
1 607 PIRSF PIRSF011502 DdrA_PduG
1 607 InterPro IPR009191 Diol dehydratase-reactivating factor large subunit
278 602 Pfam PF08841 Diol dehydratase reactivase ATPase-like domain
278 602 InterPro IPR030994 Diol dehydratase reactivase ATPase-like domain
92 256 SUPERFAMILY SSF82317 Swiveling domain of dehydratase reactivase alpha subunit
92 256 InterPro IPR028975 Diol dehydratase-reactivating factor, alpha subunit, swiveling domain superfamily
411 604 SUPERFAMILY SSF53067 Actin-like ATPase domain
411 604 InterPro IPR043129 ATPase, nucleotide binding domain
96 249 Gene3D G3DSA:3.50.30.70 Swiveling domain of dehydratase reactivase alpha subunit
96 249 InterPro IPR028975 Diol dehydratase-reactivating factor, alpha subunit, swiveling domain superfamily
3 602 Gene3D G3DSA:3.30.420.40 -
76 372 Gene3D G3DSA:3.90.470.30 -
407 583 Gene3D G3DSA:3.30.420.40 -
3 603 NCBIfam TIGR04491 diol dehydratase reactivase subunit alpha
3 603 InterPro IPR009191 Diol dehydratase-reactivating factor large subunit
250 405 SUPERFAMILY SSF53067 Actin-like ATPase domain
250 405 InterPro IPR043129 ATPase, nucleotide binding domain
468 512 Gene3D G3DSA:2.40.50.140 -
468 512 InterPro IPR012340 Nucleic acid-binding, OB-fold

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 #21
0.938
Likely same site as P2Rank 1 2.5 Å 35 shared residues 92% of smaller site
Unusual size
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Surrounding area
Site 2 FPocket #20
0.513
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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
0.967
Likely same site as FPocket 21 2.5 Å 35 shared residues 92% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.073
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Surrounding area
Site 3 P2Rank #3
0.043
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Surrounding area
Site 4 P2Rank #4
0.011
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Surrounding area
Site 5 P2Rank #5
0.007
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Surrounding area
All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 1

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
PDB 1NBW
X-ray 2.40 Å A,C
100.0% 1-607
PDBe RCSB PDBj File
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ColabFold KP13_02836
ColabFold — — full sequence — Loaded