Protein target profile

VK055_3518

gpsA

Genome: KpATCC43816 Gene: AIK82074.1 gpsA 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GUQ5
Length 330
Pocket druggability 0.971
Metabolic reactions 2
Chokepoint No
Direct ligand evidence 0 62 total records
Functional annotation 1 EC 13 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.

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 (%)
32.967 Lower values reduce human off-target concern.
Human E-value
1.47e-06
Gut microbiome similarity
3.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
95.4 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 0.971
Structure A0A0H3GUQ5
Pocket Pocket 1
P2Rank 0.92
Structure A0A0H3GUQ5
Pocket Pocket 1
ColabFold model
FPocket 0.976 · Pocket 1
P2Rank 0.953 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 164 / 4744 genomes with a hit
Prevalence 3.5%

Cross-references

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

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 99.4% of genes in this genome.

Relative network centrality 99.4% more central than 99.4% 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.

MIGAGSYGTALAITLARNGHHVVLWGHDPKHIATLQHDRCNAAFLPDVPFPDTLHLESDLATALAASRDILVVVPSHVFGQVLRQIKPLMRSDARLVWATKGLEAETGRLLQDVAREALGDDIPLAVISGPTFAKELAAGLPTAISLAATDPQFAEDLQRLLHCGKSFRVYINPDFIGVQLGGAVKNVIAIGAGMSDGIGFGANARTALITRGLVEMSRLGAALGADPETFMGMAGLGDLVLTCTDNQSRNRRFGMMLGQGMDVQSAQDKIGQVVEGYRNTKEVRVLAQRLGVEMPITEEIYQVLYCGKIAREAALTLLGRARKDERSSN

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 13 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

13
  • 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:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
  • GO:0046168 The chemical reactions and pathways resulting in the breakdown of glycerol-3-phosphate, a phosphoric monoester of glycerol.
  • 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: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:0047952 Catalysis of the reaction: sn-glycerol 3-phosphate + NAD(P)+ = glycerone phosphate + NAD(P)H + H+.
  • GO:0016616 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0141152 Catalysis of the reaction: NAD+ + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H+ + NADH.
  • GO:0141153 NADP+ + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H+ + NADPH.
  • GO:0046167 The chemical reactions and pathways resulting in the formation of glycerol-3-phosphate, a phosphoric monoester of glycerol.
  • GO:0046474 The chemical reactions and pathways resulting in the formation of glycerophospholipids, any derivative of glycerophosphate that contains at least one O-acyl, O-alkyl, or O-alkenyl group attached to the glycerol residue.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
184 330 Gene3D G3DSA:1.10.1040.10 -
184 330 InterPro IPR013328 6-phosphogluconate dehydrogenase, domain 2
175 313 Pfam PF07479 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus
175 313 InterPro IPR006109 Glycerol-3-phosphate dehydrogenase, NAD-dependent, C-terminal
1 327 PIRSF PIRSF000114 Glycerol-3-P_dh
1 327 InterPro IPR006168 Glycerol-3-phosphate dehydrogenase, NAD-dependent
1 182 FunFam G3DSA:3.40.50.720:FF:000019 Glycerol-3-phosphate dehydrogenase [NAD(P)+]
1 182 Gene3D G3DSA:3.40.50.720 -
1 314 PANTHER PTHR11728 GLYCEROL-3-PHOSPHATE DEHYDROGENASE
175 326 SUPERFAMILY SSF48179 6-phosphogluconate dehydrogenase C-terminal domain-like
175 326 InterPro IPR008927 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily
184 328 FunFam G3DSA:1.10.1040.10:FF:000001 Glycerol-3-phosphate dehydrogenase [NAD(P)+]
127 147 PRINTS PR00077 NAD-dependent glycerol-3-phosphate dehydrogenase signature
127 147 InterPro IPR006168 Glycerol-3-phosphate dehydrogenase, NAD-dependent
168 192 PRINTS PR00077 NAD-dependent glycerol-3-phosphate dehydrogenase signature
168 192 InterPro IPR006168 Glycerol-3-phosphate dehydrogenase, NAD-dependent
233 250 PRINTS PR00077 NAD-dependent glycerol-3-phosphate dehydrogenase signature
233 250 InterPro IPR006168 Glycerol-3-phosphate dehydrogenase, NAD-dependent
193 217 PRINTS PR00077 NAD-dependent glycerol-3-phosphate dehydrogenase signature
193 217 InterPro IPR006168 Glycerol-3-phosphate dehydrogenase, NAD-dependent
1 18 PRINTS PR00077 NAD-dependent glycerol-3-phosphate dehydrogenase signature
1 18 InterPro IPR006168 Glycerol-3-phosphate dehydrogenase, NAD-dependent
51 78 PRINTS PR00077 NAD-dependent glycerol-3-phosphate dehydrogenase signature
51 78 InterPro IPR006168 Glycerol-3-phosphate dehydrogenase, NAD-dependent
2 173 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
2 173 InterPro IPR036291 NAD(P)-binding domain superfamily
183 204 ProSitePatterns PS00957 NAD-dependent glycerol-3-phosphate dehydrogenase signature.
183 204 InterPro IPR006168 Glycerol-3-phosphate dehydrogenase, NAD-dependent
1 154 Pfam PF01210 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
1 154 InterPro IPR011128 Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal
1 317 Hamap MF_00394 Glycerol-3-phosphate dehydrogenase [NAD(P)+] [gpsA].
1 317 InterPro IPR006168 Glycerol-3-phosphate dehydrogenase, NAD-dependent

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 #1
0.971
Likely same site as P2Rank 2 3.3 Å 15 shared residues 100% of smaller site
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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
0.92
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.426
Likely same site as FPocket 1 3.3 Å 15 shared residues 100% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.118
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Surrounding area
Site 4 P2Rank #4
0.002
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Surrounding area
Residue sets
UniProt: Active site:195-195 Proton acceptor
UniProt: Binding site:110-110
UniProt: Binding site:12-17
UniProt: Binding site:139-139
UniProt: Binding site:141-141
UniProt: Binding site:143-143
UniProt: Binding site:15-15
UniProt: Binding site:16-16
UniProt: Binding site:195-195
UniProt: Binding site:248-248
UniProt: Binding site:258-258
UniProt: Binding site:259-259
UniProt: Binding site:259-260
UniProt: Binding site:260-260
UniProt: Binding site:283-283
UniProt: Binding site:285-285
UniProt: Binding site:36-36
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_A0A0H3GUQ5
AlphaFold DB full sequence Viewing
ColabFold VK055_3518
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.

62 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 12 records from similar proteins
Structural ligands 12 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 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
3SY PDB via homolog Detail RCSB PDB
BCP PDB via homolog Detail RCSB PDB
BOA PDB via homolog Detail RCSB PDB
CFP 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 P21695 170.1 Da LogP -1.34 TPSA 104.1 ✓ Ro5 ✓ Clean C(C(=O)COP(=O)(O)O)O
3SY RCSB PDB P21695 136.1 Da LogP -2.06 TPSA 80.9 ✓ Ro5 ✓ Clean C(C(CO)(CO)CO)O
BCP RCSB PDB P90551 233.5 Da LogP 1.77 TPSA 54.5 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)nc(nc2Cl)Br
BOA RCSB PDB P90551 215.0 Da LogP 0.82 TPSA 74.7 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)nc(nc2O)Br
CFP RCSB PDB P90551 172.6 Da LogP 1.15 TPSA 54.5 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)c(nc(n2)F)Cl
G3H RCSB PDB A0A0F6AK91 170.1 Da LogP -1.34 TPSA 104.1 ✓ Ro5 ✓ Clean C([C@H](C=O)O)OP(=O)(O)O
G3P RCSB PDB A0A0F6AK91 172.1 Da LogP -1.55 TPSA 107.2 ✓ Ro5 ✓ Clean C([C@H](COP(=O)(O)O)O)O
MYS RCSB PDB P90551 212.4 Da LogP 6.10 TPSA 0.0 1 viol. ✓ Clean CCCCCCCCCCCCCCC
NDE RCSB PDB P90551 831.5 Da LogP -4.94 TPSA 425.2 3 viol. ✓ Clean c1c[n+](cc(c1[C@H](C(=O)COP(=O)(O)O)O)C(=O)N)[C…
NH4 RCSB PDB O29390 18.0 Da LogP 0.38 TPSA 36.5 ✓ Ro5 ✓ Clean [NH4+]
PLM RCSB PDB P90551 256.4 Da LogP 5.55 TPSA 37.3 1 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)O
POP RCSB PDB P21695 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=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.