KpKP13 Protein target profile

6-phospho-beta-glucosidase bglA

Accession: KP13_02187

Gene: AHE42756.1 bglA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GY47

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Length 477

Pocket druggability (P2Rank · AlphaFold DB model) 0.968

Direct ligand evidence 0 27 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

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.97, FPocket 0.95). Use the 3D pocket comparison to verify whether they identify the same site. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.95. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.97. Review the complete evidence below

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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 (%): 39.286 Lower values reduce human off-target concern.
Human E-value: 1.25e-09
Gut microbiome similarity: 19.0% 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.

Structure confidence

ColabFold pLDDT: 97.81 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) 0.968

Structure A0A0H3GY47

Pocket Pocket 1

Druggability (FPocket) 0.954

Structure A0A0H3GY47

Pocket Pocket 10

ColabFold model

P2Rank 0.968 · Pocket 1

FPocket 0.056 · Pocket 24

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 902 / 4744 genomes with a hit

Prevalence 19.0%

Cross-references

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

Sequence

UniProt A0A0H3GY47

Sequence

Primary amino-acid sequence viewer.

MKKLTLPKDFLWGGAVAAHQVEGGWDQGGKGPSICDVLTGGAHGVPREITHQVEAGKYYPNHEAVDFYGRYKEDIKLFAEMGFKCFRTSIAWTRIFPQGDETQPNEEGLKFYDDMFDELLKYNIEPVITLSHFEMPLHLVQQYGGWTNRKVVDFFVRFAEVVFERYKHKVKYWMTFNEINNQRNWRAPLFGYCCSGVVYTEHDNPEETMYQVLHHQFVASALAVKAARRINPDMQVGCMLAMVALYPYSCKPEDVMFAQESMRERYVFTDVQLRGYYPSYVLNEWERRGFNIRMEDGDAQILREGTCAYLGFSYYMTNAVKAEGGTGDAISGFEGSVPNPHVKASDWGWQIDPVGLRYSLCELYERYQKPLFIVENGFGAYDKVEADGSINDDYRIDYLRAHIEEMIKAVTYDGVDLMGYTPWGCIDCVSFTTGQYSKRYGFIYVNKHDDGTGDMSRSRKKSFNWYKEVIASNGENL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

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: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.

22 records

Show feature table

Start	End	DB	Term	Name
3	477	FunFam	G3DSA:3.20.20.80:FF:000004	Beta-glucosidase 6-phospho-beta-glucosidase
2	470	SUPERFAMILY	SSF51445	(Trans)glycosidases
2	470	InterPro	IPR017853	Glycoside hydrolase superfamily
1	477	Gene3D	G3DSA:3.20.20.80	Glycosidases
11	475	PANTHER	PTHR10353	GLYCOSYL HYDROLASE
11	475	InterPro	IPR001360	Glycoside hydrolase family 1
5	474	Pfam	PF00232	Glycosyl hydrolase family 1
5	474	InterPro	IPR001360	Glycoside hydrolase family 1
371	379	ProSitePatterns	PS00572	Glycosyl hydrolases family 1 active site.
371	379	InterPro	IPR018120	Glycoside hydrolase family 1, active site
306	320	PRINTS	PR00131	Glycosyl hydrolase family 1 signature
306	320	InterPro	IPR001360	Glycoside hydrolase family 1
371	379	PRINTS	PR00131	Glycosyl hydrolase family 1 signature
371	379	InterPro	IPR001360	Glycoside hydrolase family 1
439	451	PRINTS	PR00131	Glycosyl hydrolase family 1 signature
439	451	InterPro	IPR001360	Glycoside hydrolase family 1
392	403	PRINTS	PR00131	Glycosyl hydrolase family 1 signature
392	403	InterPro	IPR001360	Glycoside hydrolase family 1
414	431	PRINTS	PR00131	Glycosyl hydrolase family 1 signature
414	431	InterPro	IPR001360	Glycoside hydrolase family 1
10	24	ProSitePatterns	PS00653	Glycosyl hydrolases family 1 N-terminal signature.
10	24	InterPro	IPR033132	Glycosyl hydrolases family 1, N-terminal conserved site

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

0.968

Likely same site as FPocket 10 2.9 Å 36 shared residues 100% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.121

Likely same site as FPocket 10 7.3 Å 14 shared residues 100% of smaller site

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Surrounding area

Pocket 3 P2Rank #3

0.052

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Surrounding area

Pocket 4 P2Rank #4

0.025

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Surrounding area

Pocket 5 P2Rank #5

0.015

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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 #10

0.954 Unusual size

Likely same site as P2Rank 1 2.9 Å 36 shared residues 100% of smaller site

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Surrounding area

Residue sets

UniProt: Active site:375-375 Nucleophile

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1

0.968

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Surrounding area

Pocket 2 P2Rank #2

0.031

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Surrounding area

Pocket 3 P2Rank #3

0.012

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Surrounding area

Pocket 4 P2Rank #4

0.006

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Surrounding area

Pocket 5 P2Rank #5

0.004

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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_A0A0H3GY47	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_02187	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.

27 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 15 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

BTB PDB via homolog Detail RCSB PDB

GBE PDB via homolog Detail RCSB PDB

GIM PDB via homolog Detail RCSB PDB

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.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

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](…`
BTB RCSB PDB	3VII	Q8T0W7	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`C(CO)N(CCO)C(CO)(CO)CO`
GBE RCSB PDB	3VIO	Q8T0W7	414.5 Da LogP -3.30 TPSA 160.2	✓ Ro5	✓ Clean	`C1CN(CCN1CCCS(=O)(=O)O)CCO[C@H]2[C@@H]([C@H]([C…`
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)…`
GOI RCSB PDB	3VIP	Q8T0W7	525.6 Da LogP 1.13 TPSA 109.1	1 viol.	✓ Clean	`c1ccc2c(c1)C=Cc3ccccc3N2CCCN4CCN(CC4)CCO[C@H]5[…`
HBO RCSB PDB	3AIQ	Q1XH05	211.2 Da LogP 0.13 TPSA 79.2	✓ Ro5	✓ Clean	`COc1ccc2c(c1)O[C@H](C(=O)N2O)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`
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]…`
NOJ RCSB PDB	3VIG	Q8T0W7	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`
ONB RCSB PDB	3VIP	Q8T0W7	193.2 Da LogP 3.91 TPSA 12.0	✓ Ro5	✓ Clean	`c1ccc2c(c1)C=Cc3ccccc3N2`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC1615342 ZINC	1.000	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`OCCN(CCO)C(CO)(CO)CO`
ZINC2018620 ZINC	1.000	211.2 Da LogP 0.13 TPSA 79.2	✓ Ro5	✓ Clean	`COc1ccc2c(c1)O[C@@H](O)C(=O)N2O`
ZINC2018621 ZINC	1.000	211.2 Da LogP 0.13 TPSA 79.2	✓ Ro5	✓ Clean	`COc1ccc2c(c1)O[C@H](O)C(=O)N2O`
ZINC39238166 ZINC	0.640	207.3 Da LogP 4.22 TPSA 12.0	✓ Ro5	✓ Clean	`Cc1ccc2c(c1)C=Cc1ccccc1N2`
ZINC5948252 ZINC	0.600	221.3 Da LogP 3.42 TPSA 29.1	✓ Ro5	✓ Clean	`O=C1Nc2ccccc2C=Cc2ccccc21`
ZINC21981303 ZINC	0.558	363.5 Da LogP 3.31 TPSA 30.0	✓ Ro5	✓ Clean	`OCCN1CCN(CCCN2c3ccccc3C=Cc3ccccc32)CC1`
ZINC100350904 ZINC	0.556	273.3 Da LogP 3.46 TPSA 46.2	✓ Ro5	Alert	`O=C1C(=C2C=Cc3ccccc3N2)C(=O)c2ccccc21`
ZINC68565001 ZINC	0.529	204.3 Da LogP 4.34 TPSA 0.0	✓ Ro5	✓ Clean	`C1=Cc2ccccc2C=Cc2ccccc21`
ZINC2334905 ZINC	0.522	261.4 Da LogP 1.10 TPSA 63.9	✓ Ro5	✓ Clean	`CC(C)CCN(CCC(C)C)C(CO)(CO)CO`
ZINC3159953 ZINC	0.522	261.4 Da LogP 1.38 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCN(CCCCC)C(CO)(CO)CO`
ZINC114003466 ZINC	0.520	207.3 Da LogP 3.78 TPSA 12.0	✓ Ro5	✓ Clean	`C1=Cc2ccccc2NCc2ccccc21`
ZINC16123955 ZINC	0.500	204.2 Da LogP -2.82 TPSA 101.8	✓ Ro5	✓ Clean	`CC(=O)NC[C@H]1NC[C@H](O)[C@@H](O)[C@@H]1O`
ZINC5297554 ZINC	0.500	289.5 Da LogP 2.16 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCCN(CCCCCC)C(CO)(CO)CO`
ZINC97941822 ZINC	0.500	317.5 Da LogP 2.94 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCCCN(CCCCCCC)C(CO)(CO)CO`
ZINC97942927 ZINC	0.500	373.6 Da LogP 4.51 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCCCCCN(CCCCCCCCC)C(CO)(CO)CO`

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.