Protein target profile

VK055_4445

6-phospho-beta-glucosidase gmuD

Genome: KpATCC43816 Gene: AIK82988.1 gmuD2 3D evidence: AlphaFold DB model + ColabFold model Metabolism 20 reactions UniProt A0A0H3GXA3
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Length 466
Pocket druggability 0.983
Metabolic reactions 20
Chokepoint Yes
Direct ligand evidence 0 36 total records
Functional annotation 0 EC 5 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

Metabolic bottleneck Catalyzes a reaction that is the only producer or consumer of a metabolite in the imported metabolic model. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.95. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Human similarity Top human hit identity: 32.843%. This target also has a predicted binding pocket (FPocket 0.98) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 106 of 4744 screened genomes (2.2%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.98) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.98, 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 coverage

Core evidence streams are available for this target.
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 (%)
32.843 Lower values reduce human off-target concern.
Human E-value
4.3499999999999995e-28
Gut microbiome similarity
2.2% 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
97.2 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 0.983
Structure A0A0H3GXA3
Pocket Pocket 1
P2Rank 0.95
Structure A0A0H3GXA3
Pocket Pocket 1
ColabFold model
FPocket 0.978 · Pocket 1
P2Rank 0.947 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 106 / 4744 genomes with a hit
Prevalence 2.2%

Cross-references

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

Sequence

UniProt A0A0H3GXA3

Chemistry

ChEMBL CHEMBL157924

Pathways

BioCyc RXN0-6994 BioCyc RXN0-7002 KEGG R00839 BioCyc 6-PHOSPHO-BETA-GLUCOSIDASE-RXN BioCyc 6-PHOSPHO-BETA-GLUCOSIDASE-RXN-CPD-15978/WATER//ALPHA-GLC-6-P/ALPHA-GLUCOSE.45. BioCyc 6-PHOSPHO-BETA-GLUCOSIDASE-RXN-CPD-15978/WATER//ALPHA-GLC-6-P/GLC.35. BioCyc 6-PHOSPHO-BETA-GLUCOSIDASE-RXN-CPD-15978/WATER//ALPHA-GLC-6-P/Glucopyranose.45. BioCyc 6-PHOSPHO-BETA-GLUCOSIDASE-RXN-CPD-15978/WATER//D-glucopyranose-6-phosphate/ALPHA-GLUCOSE.59. BioCyc 6-PHOSPHO-BETA-GLUCOSIDASE-RXN-CPD-15978/WATER//D-glucopyranose-6-phosphate/GLC.49. BioCyc 6-PHOSPHO-BETA-GLUCOSIDASE-RXN-CPD-15978/WATER//GLC-6-P/ALPHA-GLUCOSE.39. BioCyc 6-PHOSPHO-BETA-GLUCOSIDASE-RXN-CPD-15978/WATER//GLC-6-P/GLC.29. BioCyc 6-PHOSPHO-BETA-GLUCOSIDASE-RXN-CPD-15978/WATER//GLC-6-P/Glucopyranose.39. BioCyc 6-PHOSPHO-BETA-GLUCOSIDASE-RXN-CPD-507/WATER//ALPHA-GLC-6-P/ALPHA-GLUCOSE.43. BioCyc 6-PHOSPHO-BETA-GLUCOSIDASE-RXN-CPD-507/WATER//ALPHA-GLC-6-P/GLC.33. BioCyc 6-PHOSPHO-BETA-GLUCOSIDASE-RXN-CPD-507/WATER//ALPHA-GLC-6-P/Glucopyranose.43. BioCyc 6-PHOSPHO-BETA-GLUCOSIDASE-RXN-CPD-507/WATER//D-glucopyranose-6-phosphate/ALPHA-GLUCOSE.57. BioCyc 6-PHOSPHO-BETA-GLUCOSIDASE-RXN-CPD-507/WATER//D-glucopyranose-6-phosphate/GLC.47. BioCyc 6-PHOSPHO-BETA-GLUCOSIDASE-RXN-CPD-507/WATER//D-glucopyranose-6-phosphate/Glucopyranose.57. BioCyc 6-PHOSPHO-BETA-GLUCOSIDASE-RXN-CPD-507/WATER//GLC-6-P/ALPHA-GLUCOSE.37. BioCyc 6-PHOSPHO-BETA-GLUCOSIDASE-RXN-CPD-507/WATER//GLC-6-P/GLC.27. BioCyc 6-PHOSPHO-BETA-GLUCOSIDASE-RXN-CPD-507/WATER//GLC-6-P/Glucopyranose.37.

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a producing chokepoint reaction in Starch and sucrose metabolism.

Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Chokepoint gene
Pathways
Starch and sucrose metabolism
Catalyzed reactions

20 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.

MQQYQFPQGFLWGAAASGPQTEGVTNKRHRSIWDSWFAEQPERFYQQVGPQTVCDTYHQYPQDVALMKQTGFNSFRTSIQWSRLIADLETGAPDPDAVRFYHAYLDEMIANGIEPMINLYHFDMPEALQKQYGGFESAHVAELFARFARTAFSLFGHKVKYWITFNEPIVPVEGGYLYDFHYPCKKDGRLAAQVAFNIMLAHAKAVTAYRELALAGEIGVVLNLTPSYTLTDSDADKKAAGYADLFFNRSFLDPLVKHEFPKALCEILAAHDCLPTTSKDDAALILSADIDFLGVNYYVPRRVKARESEYDLDYFTPEYYFENAVNPQGRFNPYRDNNEILPQAIYDIAANIRDNYGNIKWYLAEIGIAMDRQSEGEPGADGVIDDTFRIQLMEEHLVQLHRAIADGANCFGVHQWTFIDNWSWINAFKRRYGFWRLDLETGERQIKRNALWFAELASSNGFTSDK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0008422 Catalysis of the hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose.
  • GO:0016052 The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
431 443 PRINTS PR00131 Glycosyl hydrolase family 1 signature
431 443 InterPro IPR001360 Glycoside hydrolase family 1
407 424 PRINTS PR00131 Glycosyl hydrolase family 1 signature
407 424 InterPro IPR001360 Glycoside hydrolase family 1
289 303 PRINTS PR00131 Glycosyl hydrolase family 1 signature
289 303 InterPro IPR001360 Glycoside hydrolase family 1
386 397 PRINTS PR00131 Glycosyl hydrolase family 1 signature
386 397 InterPro IPR001360 Glycoside hydrolase family 1
3 462 Pfam PF00232 Glycosyl hydrolase family 1
3 462 InterPro IPR001360 Glycoside hydrolase family 1
4 462 SUPERFAMILY SSF51445 (Trans)glycosidases
4 462 InterPro IPR017853 Glycoside hydrolase superfamily
3 463 FunFam G3DSA:3.20.20.80:FF:000004 Beta-glucosidase 6-phospho-beta-glucosidase
5 463 PANTHER PTHR10353 GLYCOSYL HYDROLASE
5 463 InterPro IPR001360 Glycoside hydrolase family 1
3 462 Gene3D G3DSA:3.20.20.80 Glycosidases

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.

Download VMD script Full viewer

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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
0.983
Likely same site as P2Rank 2 0.5 Å 21 shared residues 100% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.95
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.896
Likely same site as FPocket 1 0.5 Å 21 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.113
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.046
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.04
Show in viewer
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_A0A0H3GXA3
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4445
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.

36 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 8 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 1 direct and transferred ChEMBL records
Proposed compounds 28 similarity-based ZINC candidates
Best available ligand signal
8P2 PDB via homolog 187.2 Da · LogP -1.68 · TPSA 101.4 Open detail RCSB PDB
AM3 PDB via homolog Detail RCSB PDB
GIM PDB via homolog Detail RCSB PDB
IFM PDB via homolog Detail RCSB PDB
JAZ 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
8P2 RCSB PDB
5N6T
Q08638 187.2 Da LogP -1.68 TPSA 101.4 ✓ Ro5 ✓ Clean C(C1C(C(C(C2C1O2)O)O)O)[N+]#N
AM3 RCSB PDB
2WC3
Q08638 316.4 Da LogP -0.18 TPSA 105.8 ✓ Ro5 ✓ Clean CCCCCCCC/N=C\1/N2[C@H](CO1)[C@@H]([C@@H]([C@H](…
GIM RCSB PDB
7BZM
Q75I93 201.2 Da LogP -2.40 TPSA 100.6 ✓ Ro5 ✓ Clean c1c[n+]2c([nH]1)[C@@H]([C@H]([C@@H]([C@H]2CO)O)…
IFM RCSB PDB
1OIF
Q08638 147.2 Da LogP -2.08 TPSA 72.7 ✓ Ro5 ✓ Clean C1[C@@H]([C@H]([C@@H](CN1)O)O)CO
JAZ RCSB PDB
5FOO
Q99YP9 274.2 Da LogP -3.47 TPSA 167.9 1 viol. ✓ Clean C(C1[C@H]([C@@H](C([C@H]([C@@H]1O)O)O)O)O)OP(=O…
JJW RCSB PDB
6QWI
P22073 348.4 Da LogP 0.05 TPSA 101.7 ✓ Ro5 ✓ Clean CCOCCOc1ccc(cc1)c2cn(nn2)C[C@H]3[C@@H]([C@@H](C…
JSK RCSB PDB
6R4K
P22073 391.4 Da LogP -0.43 TPSA 149.9 ✓ Ro5 Alert [H]/N=N/NCCOCCOc1ccc(cc1)c2cn(nn2)C[C@H]3[C@@H]…

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.