Protein target profile

VK055_4866

glycerol-3-phosphate dehydrogenase, anaerobic, Csubunit

Genome: KpATCC43816 Gene: AIK83393.1 glpC 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GSZ6
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Length 392
Pocket druggability 0.995
Metabolic reactions 2
Chokepoint No
Functional annotation 0 EC 8 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 99.8% 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. 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 256 of 4744 screened genomes (5.4%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.99) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.99, 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.

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
5.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
24.065 Higher values support similarity to known essential genes.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
95.71 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 0.995
Structure A0A0H3GSZ6
Pocket Pocket 6
P2Rank 0.974
Structure A0A0H3GSZ6
Pocket Pocket 1
ColabFold model
FPocket 0.997 · Pocket 8
P2Rank 0.971 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 256 / 4744 genomes with a hit
Prevalence 5.4%

Cross-references

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

Sequence

UniProt A0A0H3GSZ6

Pathways

BioCyc RXN-15740 BioCyc GLYC3PDEHYDROG-RXN

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 99.8% of genes in this genome, no human homolog detected.

Relative network centrality 99.8% more central than 99.8% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

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.

MNDTRFESCIKCTVCTTTCPVSRVNPRYPGPKQAGPDGERLRLKDGALYDEALKYCINCKRCEVACPSDVKIGDIIQRARAQYGQQKPTLRDAILSHTDLMGTLSTPFAPLVNAATGLKPVRRLLDATLNIDHRRTLPKYGFGTFRRAYRQLAARQKQYSEPVAFFHGCYVNYNHPQLGKDLIRVVNALGTGVQLLSKEKCCGVPLIANGFFDKARKQAQSNVAAMRENTLPIIATSSTCAFTLRDEYPHLLDVDNSDLRDRVELATRWIWKQLAAGRTLPLRPLPLKVVYHTPCHMEKMGWSLYTLELLRLIPGLQLEVLDSQCCGIAGTYGFKTENYAVSQAIGAPLFRQIEESGADLVVTDCETCKWQIEMSTSKRCEHPLTVLAQALV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

8
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0009061 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.
  • GO:0009331 An enzyme complex that catalyzes the oxidation of sn-glycerol 3-phosphate to dihydroxyacetone phosphate, with concurrent reduction of flavin adenine dinucleotide (FAD) to FADH2. In E. coli, the complex is either a GlpA-GlpB-GlpC heterotrimer that functions in anaerobic conditions, or a GlpD homodimer that functions in aerobic conditions.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0046872 Binding to a metal ion.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
6 69 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
56 67 ProSitePatterns PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature.
56 67 InterPro IPR017900 4Fe-4S ferredoxin, iron-sulphur binding, conserved site
45 70 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
45 70 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
6 83 SUPERFAMILY SSF46548 alpha-helical ferredoxin
289 372 Pfam PF02754 Cysteine-rich domain
289 372 InterPro IPR004017 Cysteine-rich domain
163 245 Pfam PF02754 Cysteine-rich domain
163 245 InterPro IPR004017 Cysteine-rich domain
6 69 Pfam PF13183 4Fe-4S dicluster domain
3 89 Gene3D G3DSA:1.10.1060.10 -
3 89 InterPro IPR009051 Alpha-helical ferredoxin
1 29 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
1 29 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
3 89 FunFam G3DSA:1.10.1060.10:FF:000008 Glycerol-3-phosphate dehydrogenase, anaerobic, C subunit
3 391 PANTHER PTHR32479 GLYCOLATE OXIDASE IRON-SULFUR SUBUNIT
3 391 NCBIfam TIGR03379 anaerobic glycerol-3-phosphate dehydrogenase subunit GlpC
3 391 InterPro IPR017753 Glycerol-3-phosphate dehydrogenase, GlpC subunit

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 #6
0.995
Likely same site as P2Rank 1 0.5 Å 35 shared residues 95% of smaller site
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
0.974
Likely same site as FPocket 6 0.5 Å 35 shared residues 95% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.374
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Surrounding area
Site 3 P2Rank #3
0.169
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Surrounding area
Site 4 P2Rank #4
0.079
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Surrounding area
Site 5 P2Rank #5
0.038
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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_A0A0H3GSZ6
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4866
ColabFold — — full sequence — Loaded