Genome KpKP13

Protein target profile

Anaerobic glycerol-3-phosphate dehydrogenase subunit A

Accession: KP13_00962

Gene: AHE43508.1 glpA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GW84
Length 540
Pocket druggability (P2Rank · AlphaFold DB model) 0.975
Direct ligand evidence 0 51 total records
Functional annotation 1 EC 10 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 (%)
50.0 Lower values reduce human off-target concern.
Human E-value
5.53e-06
Gut microbiome similarity
5.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
93.3 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) 0.975
Structure A0A0H3GW84
Pocket Pocket 1
Druggability (FPocket) 0.822
Structure A0A0H3GW84
Pocket Pocket 5
ColabFold model
P2Rank 0.982 · Pocket 1
FPocket 0.677 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 253 / 4744 genomes with a hit
Prevalence 5.3%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MTGRLDSEVIIIGGGATGAGIARDCARRGLRTLLIERHDIATGATGRNHGLLHSGARYAVTDNESARECISENRILRRIARHCIEPTNGLFITLPEDDLAWQQTFIDACQQAGIEATPLSPQEALRREPAVNPTLLGAVQVPDGTIDPFRLTAANMLDAREHGAQILTGCEVTGLLRRGDRVCGVQVYDRQLHQARTLYAGMVVNAAGIWGQRIAEYADLRITMFPAKGSLLILDHRINNLVINRCRKPADADILVPGDTISLIGTTSMHIPYDEIDDNRVTAAEVDTLLREGEKLAPVMGRTRILRAYSGVRPLVASDNDPSGRSVSRGIVLLDHAQRDGMEGFITITGGKLMTYRLMAEWATDAVCRKLGNTTPCTTAEAPLPGSQEPTESTLQKIISLPTPLRGSAVYRHGDRTPSWLGDSRQHRSLVCECEAVTAGEVKYAVENLAVNTLLDLRRRTRIGMGTCQGELCACRAAGLLQRFNVTTPAQSLTQLSEFLNERWKGVQPIAWGDALRESEFTRWVYLGLCGLPQEHRDEV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

10
  • 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:0010181 Binding to flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
  • 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:0006072 The chemical reactions and pathways involving glycerol-3-phosphate, a phosphoric monoester of glycerol.
  • 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.
  • GO:0004368 Catalysis of the reaction: sn-glycerol 3-phosphate + a quinone = glycerone phosphate + a quinol.
  • GO:0046174 The chemical reactions and pathways resulting in the breakdown of a polyol, any alcohol containing three or more hydroxyl groups attached to saturated carbon atoms.
  • GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
  • GO:0019563 The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
  • GO:0046168 The chemical reactions and pathways resulting in the breakdown of glycerol-3-phosphate, a phosphoric monoester of glycerol.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

38 records
Show feature table
Start End DB Term Name
418 491 Gene3D G3DSA:1.10.10.1100 -
418 491 InterPro IPR041854 BFD-like [2Fe-2S]-binding domain superfamily
12 29 ProSitePatterns PS00977 FAD-dependent glycerol-3-phosphate dehydrogenase signature 1.
12 29 InterPro IPR000447 FAD-dependent glycerol-3-phosphate dehydrogenase
312 392 FunFam G3DSA:3.50.50.60:FF:000096 Glycerol-3-phosphate dehydrogenase
8 536 NCBIfam TIGR03377 anaerobic glycerol-3-phosphate dehydrogenase subunit GlpA
8 536 InterPro IPR017752 Glycerol-3-phosphate dehydrogenase, GlpA subunit
8 525 PANTHER PTHR11985 GLYCEROL-3-PHOSPHATE DEHYDROGENASE
8 525 InterPro IPR000447 FAD-dependent glycerol-3-phosphate dehydrogenase
2 120 FunFam G3DSA:3.50.50.60:FF:000102 Glycerol-3-phosphate dehydrogenase
9 357 Pfam PF01266 FAD dependent oxidoreductase
9 357 InterPro IPR006076 FAD dependent oxidoreductase
3 117 Gene3D G3DSA:3.50.50.60 -
3 117 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
122 248 Gene3D G3DSA:3.50.50.60 -
122 248 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
418 490 FunFam G3DSA:1.10.10.1100:FF:000003 Glycerol-3-phosphate dehydrogenase
298 388 Gene3D G3DSA:3.50.50.60 -
298 388 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
80 92 PRINTS PR01001 FAD-dependent glycerol-3-phosphate dehydrogenase family signature
80 92 InterPro IPR000447 FAD-dependent glycerol-3-phosphate dehydrogenase
20 30 PRINTS PR01001 FAD-dependent glycerol-3-phosphate dehydrogenase family signature
20 30 InterPro IPR000447 FAD-dependent glycerol-3-phosphate dehydrogenase
36 48 PRINTS PR01001 FAD-dependent glycerol-3-phosphate dehydrogenase family signature
36 48 InterPro IPR000447 FAD-dependent glycerol-3-phosphate dehydrogenase
345 357 PRINTS PR01001 FAD-dependent glycerol-3-phosphate dehydrogenase family signature
345 357 InterPro IPR000447 FAD-dependent glycerol-3-phosphate dehydrogenase
7 19 PRINTS PR01001 FAD-dependent glycerol-3-phosphate dehydrogenase family signature
7 19 InterPro IPR000447 FAD-dependent glycerol-3-phosphate dehydrogenase
309 315 PRINTS PR01001 FAD-dependent glycerol-3-phosphate dehydrogenase family signature
309 315 InterPro IPR000447 FAD-dependent glycerol-3-phosphate dehydrogenase
350 360 ProSitePatterns PS00978 FAD-dependent glycerol-3-phosphate dehydrogenase signature 2.
430 483 CDD cd19946 GlpA-like_Fer2_BFD-like
224 315 SUPERFAMILY SSF54373 FAD-linked reductases, C-terminal domain
430 482 Pfam PF04324 BFD-like [2Fe-2S] binding domain
430 482 InterPro IPR007419 BFD-like [2Fe-2S]-binding domain
8 320 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
8 320 InterPro IPR036188 FAD/NAD(P)-binding 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
0.975
Likely same site as FPocket 1 1.9 Å 50 shared residues 94% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.905
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Surrounding area
Pocket 3 P2Rank #3
0.11
Likely same site as FPocket 5 0.9 Å 13 shared residues 100% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.05
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Surrounding area
Pocket 5 P2Rank #5
0.034
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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 #5
0.822 Unusual size
Likely same site as P2Rank 3 0.9 Å 13 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #1
0.36 Unusual size
Likely same site as P2Rank 1 1.9 Å 50 shared residues 94% of smaller site
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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_A0A0H3GW84
AlphaFold DB full sequence Viewing
ColabFold KP13_00962
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
THG PDB via homolog 445.4 Da · LogP -0.28 · TPSA 211.6 Open detail RCSB PDB
ZINC4228235 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC4228236 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC4228237 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC4228238 ZINC proposed compound · Tanimoto 1.000 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
THG RCSB PDB Q63342 445.4 Da LogP -0.28 TPSA 211.6 1 viol. ✓ Clean c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@H]2C…

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.