Protein target profile

VK055_3380

6-phospho-alpha-glucosidase

Genome: KpATCC43816 Gene: aglB AIK81937.1 3D evidence: Experimental + ColabFold model Metabolism 9 reactions UniProt Q9AGA6
Length 440
Pocket druggability 0.681
Metabolic reactions 9
Chokepoint No
Direct ligand evidence 1 52 total records
Functional annotation 1 EC 7 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
No hit
Gut microbiome similarity
9.1% 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
95.72 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 0.681
Structure 6DUX
Pocket Pocket 1
P2Rank 0.926
Structure 6DUX
Pocket Pocket 1
ColabFold model
FPocket 0.443 · Pocket 4
P2Rank 0.969 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 432 / 4744 genomes with a hit
Prevalence 9.1%

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: no human homolog detected.

Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Catalyzed reactions

9 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.

MKKFSVVIAGGGSTFTPGIVLMLLANQDRFPLRSLKFYDNDGARQETIAEACKVILKEQAPEIEFSYTTDPQAAFTDVDFVMAHIRVGKYPMREQDEKIPLRHGVLGQETCGPGGIAYGMRSIGGVLELVDYMEKYSPNAWMLNYSNPAAIVAEATRRLRPNAKILNICDMPIGIEGRMAQIVGLKDRKQMRVRYYGLNHFGWWTSIEDLDGNDLMPKLREYVAKYGYVPPSNDPHTEASWNDTFAKAKDVQALDPQTMPNTYLKYYLFPDYVVAHSNPERTRANEVMDHREKNVFSACRAIIAAGKSTAGDLEIDEHASYIVDLATAIAFNTQERMLLIVPNNGAIHNFDADAMVEIPCLVGHNGPEPLTVGDIPHFQKGLMSQQVAVEKLVVDAWEQRSYHKLWQAITLSKTVPSASVAKAILDDLIAANKDYWPELH

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0004553 Catalysis of the hydrolysis of any O-glycosyl bond.
  • 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: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:0050081 Catalysis of the reaction: H2O + maltose 6'-phosphate = D-glucose + D-glucose 6-phosphate.
  • GO:0046872 Binding to a metal ion.
  • GO:0005985 The chemical reactions and pathways involving sucrose, the disaccharide fructofuranosyl-glucopyranoside.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

36 records
Show feature table
Start End DB Term Name
6 25 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
167 440 Gene3D G3DSA:3.90.110.10 -
167 440 InterPro IPR015955 Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal
138 169 ProSitePatterns PS01324 Glycosyl hydrolases family 4 signature.
138 169 InterPro IPR019802 Glycoside hydrolase, family 4, conserved site
5 27 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 439 PANTHER PTHR32092 6-PHOSPHO-BETA-GLUCOSIDASE-RELATED
1 439 InterPro IPR001088 Glycoside hydrolase, family 4
3 164 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
3 164 InterPro IPR036291 NAD(P)-binding domain superfamily
1 166 Gene3D G3DSA:3.40.50.720 -
6 184 Pfam PF02056 Family 4 glycosyl hydrolase
6 184 InterPro IPR001088 Glycoside hydrolase, family 4
4 440 CDD cd05298 GH4_GlvA_pagL_like
26 440 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 166 FunFam G3DSA:3.40.50.720:FF:000295 6-phospho-alpha-glucosidase
168 439 SUPERFAMILY SSF56327 LDH C-terminal domain-like
168 439 InterPro IPR015955 Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal
138 155 PRINTS PR00732 Glycosyl hydrolase family 4 signature
138 155 InterPro IPR001088 Glycoside hydrolase, family 4
191 203 PRINTS PR00732 Glycosyl hydrolase family 4 signature
191 203 InterPro IPR001088 Glycoside hydrolase, family 4
5 20 PRINTS PR00732 Glycosyl hydrolase family 4 signature
5 20 InterPro IPR001088 Glycoside hydrolase, family 4
74 90 PRINTS PR00732 Glycosyl hydrolase family 4 signature
74 90 InterPro IPR001088 Glycoside hydrolase, family 4
95 108 PRINTS PR00732 Glycosyl hydrolase family 4 signature
95 108 InterPro IPR001088 Glycoside hydrolase, family 4
164 175 PRINTS PR00732 Glycosyl hydrolase family 4 signature
164 175 InterPro IPR001088 Glycoside hydrolase, family 4
109 129 PRINTS PR00732 Glycosyl hydrolase family 4 signature
109 129 InterPro IPR001088 Glycoside hydrolase, family 4
167 440 FunFam G3DSA:3.90.110.10:FF:000010 6-phospho-alpha-glucosidase
195 415 Pfam PF11975 Family 4 glycosyl hydrolase C-terminal domain
195 415 InterPro IPR022616 Glycosyl hydrolase, family 4, C-terminal

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
0.681
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Surrounding area
Site 2 FPocket #17
0.269
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Surrounding area
Site 3 FPocket #21
0.235
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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
0.926
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Surrounding area
Site 2 P2Rank #2
0.046
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Surrounding area
Site 3 P2Rank #3
0.042
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Surrounding area
Site 4 P2Rank #4
0.03
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Surrounding area
Site 5 P2Rank #5
0.009
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Surrounding area
All structural evidence 2 experimental · 1 predicted

Structural evidence

2 + 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 6DUX
X-ray 2.25 Å A,B
99.8% 2-440
Viewing
PDB 6DVV
X-ray 2.25 Å A,B
99.8% 2-440
Loaded
ColabFold VK055_3380
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.

52 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 1 same-protein records
Transferred evidence 1 records from similar proteins
Structural ligands 2 1 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
LMR PDB co-crystal 134.1 Da · LogP -1.09 · TPSA 94.8 Open detail RCSB PDB
G6P PDB via homolog Detail RCSB PDB
ZINC100351935 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC1529564 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC1532533 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.

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Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
LMR RCSB PDB 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)O)C(=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.