Protein target profile

KP13_03192

Periplasmic beta-glucosidase

Genome: KpKP13 Gene: bglX AHE43595.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQV7
Length 755
Pocket druggability 0.535
Direct ligand evidence 0 55 total records
Functional annotation 1 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.

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
1.9% 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
Periplasmic

Structure confidence

ColabFold pLDDT
97.12 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 0.535
Structure A0A0H3GQV7
Pocket Pocket 2
P2Rank 0.677
Structure A0A0H3GQV7
Pocket Pocket 1
ColabFold model
FPocket 0.422 · Pocket 24
P2Rank 0.829 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 88 / 4744 genomes with a hit
Prevalence 1.9%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MSLALQPALADELFGNHPLTPQARDAFVTDLLKKMTVDEKIGQLRLISVGPDNPKEAIREMIKNGQVGAIFNTVTRPDIRVMQDQVMQLSRLKIPLFFAYDVLHGQRTVFPISLGLASSFNLDAVKTVGRVSAYEAADDGLNMTWAPMVDVSRDPRWGRASEGFGEDTYLTTMMGQAMVESMQGKSPADRYSVMTSVKHFAAYGAVEGGKEYNTVDMSPQRLFNDYMPPYKAGLDAGSGAVMVALNSLNGTPATSDSWLLKDVLRDQWGFKGITVSDHGAIKELIKHGVASDPEDAVRVALKSGINMSMSDEYYSKYLPGLVKSGKVTMAELDDATRHVLNVKYDMGLFNDPYSHLGPKDSDPQDTNAESRLHRKEAREVARESLVLLKNRLDTLPLKKSGTIAVVGALADSKRDMMGSWSAAGVADQSVTVLTGIKEALGDNGKVIYAKGANVTDDKGIVDFLNLYENAVQVDPRSPQEMIDEAVAAAKQSDVVVAVVGEAQGMAHEASSRTDITLPQSQRNLIAALKATGKPLVLVLMNGRPLALVKEDQQADALLETWFAGTEGGHAIADVLFGDYNPSGKLPMSFPRSVGQIPTYYSHLNTGRPYNPEKPNKYTSRYFDEANGPLYPFGYGLSYTTFSVSDVNMSSATMPRDGSVTASVQVTNTGNREGATVIQLYLQDVTASMSRPVKMLRGFKKVTLKPGETQTVSFPIDVDALKFWNQQMKYVAEPGKFNVFIGVDSARVKQSEFELL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • 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:0004553 Catalysis of the hydrolysis of any O-glycosyl bond.
  • GO:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
  • GO:0008422 Catalysis of the hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose.
  • GO:0009251 The chemical reactions and pathways resulting in the breakdown of glucans, polysaccharides consisting only of glucose residues.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

34 records
Show feature table
Start End DB Term Name
22 638 PANTHER PTHR30620 PERIPLASMIC BETA-GLUCOSIDASE-RELATED
23 384 SUPERFAMILY SSF51445 (Trans)glycosidases
23 384 InterPro IPR017853 Glycoside hydrolase superfamily
36 342 Pfam PF00933 Glycosyl hydrolase family 3 N terminal domain
36 342 InterPro IPR001764 Glycoside hydrolase, family 3, N-terminal
110 129 PRINTS PR00133 Glycosyl hydrolase family 3 signature
110 129 InterPro IPR001764 Glycoside hydrolase, family 3, N-terminal
156 172 PRINTS PR00133 Glycosyl hydrolase family 3 signature
156 172 InterPro IPR001764 Glycoside hydrolase, family 3, N-terminal
193 209 PRINTS PR00133 Glycosyl hydrolase family 3 signature
193 209 InterPro IPR001764 Glycoside hydrolase, family 3, N-terminal
263 281 PRINTS PR00133 Glycosyl hydrolase family 3 signature
263 281 InterPro IPR001764 Glycoside hydrolase, family 3, N-terminal
91 107 PRINTS PR00133 Glycosyl hydrolase family 3 signature
91 107 InterPro IPR001764 Glycoside hydrolase, family 3, N-terminal
263 280 ProSitePatterns PS00775 Glycosyl hydrolases family 3 active site.
263 280 InterPro IPR019800 Glycoside hydrolase, family 3, active site
20 362 FunFam G3DSA:3.20.20.300:FF:000005 Periplasmic beta-glucosidase
675 744 SMART SM01217 Fn3_like_2
675 744 InterPro IPR026891 Fibronectin type III-like domain
371 638 FunFam G3DSA:3.40.50.1700:FF:000004 Periplasmic beta-glucosidase
19 362 Gene3D G3DSA:3.20.20.300 -
19 362 InterPro IPR036962 Glycoside hydrolase, family 3, N-terminal domain superfamily
639 754 Gene3D G3DSA:2.60.40.10 Immunoglobulins
639 754 InterPro IPR013783 Immunoglobulin-like fold
371 638 Gene3D G3DSA:3.40.50.1700 -
371 638 InterPro IPR036881 Glycoside hydrolase family 3 C-terminal domain superfamily
385 638 Pfam PF01915 Glycosyl hydrolase family 3 C-terminal domain
385 638 InterPro IPR002772 Glycoside hydrolase family 3 C-terminal domain
676 743 Pfam PF14310 Fibronectin type III-like domain
676 743 InterPro IPR026891 Fibronectin type III-like domain
385 641 SUPERFAMILY SSF52279 Beta-D-glucan exohydrolase, C-terminal domain
385 641 InterPro IPR036881 Glycoside hydrolase family 3 C-terminal domain superfamily
640 755 FunFam G3DSA:2.60.40.10:FF:000495 Periplasmic beta-glucosidase

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

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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 #2
0.535
Likely same site as P2Rank 1 3.1 Å 16 shared residues 80% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #14
0.36
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.677
Likely same site as FPocket 2 3.1 Å 16 shared residues 80% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.548
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.526
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.224
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.158
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_A0A0H3GQV7
AlphaFold DB full sequence Viewing
ColabFold KP13_03192
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.

55 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 1 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
6BV PDB via homolog 358.4 Da · LogP -4.68 · TPSA 180.3 Open detail RCSB PDB
DTT PDB via homolog Detail RCSB PDB
LAM PDB via homolog Detail RCSB PDB
NOJ PDB via homolog Detail RCSB PDB
IFM ChEMBL via homolog · pchembl 8.15 (~7.1 nM) Detail ChEMBL

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
6BV RCSB PDB Q9XEI3 358.4 Da LogP -4.68 TPSA 180.3 2 viol. ✓ Clean C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)O)S[C@H…
DTT RCSB PDB A0A0H0XV02 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
LAM RCSB PDB Q9XEI3 641.6 Da LogP -4.86 TPSA 291.6 3 viol. ✓ Clean c1cc(ccc1[N+](=O)[O-])OC2C(C(C(C(O2)CO)O)O[C@H]…
NOJ RCSB PDB Q9I311 163.2 Da LogP -2.97 TPSA 93.0 ✓ Ro5 ✓ Clean C1[C@@H]([C@H]([C@@H]([C@H](N1)CO)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.