Protein target profile

KP13_03814

6-phospho-beta-glucosidase bglA

Genome: KpKP13 Gene: AHE43299.1 3D evidence: AlphaFold DB model + ColabFold model UniProt W9BC02

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Length 477

Pocket druggability 0.78

Direct ligand evidence 0 38 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.

Main supporting evidence

Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.78, P2Rank 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 0.78. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.95. 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 (%): 29.98 Lower values reduce human off-target concern.
Human E-value: 7.299999999999999e-47
Gut microbiome similarity: 20.8% 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: 97.98 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 0.78

Structure W9BC02

Pocket Pocket 2

P2Rank 0.95

Structure W9BC02

Pocket Pocket 1

ColabFold model

FPocket 0.401 · Pocket 21

P2Rank 0.957 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 986 / 4744 genomes with a hit

Prevalence 20.8%

Cross-references

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

Sequence

UniProt W9BC02

Chemistry

ChEMBL CHEMBL157924

Sequence

Primary amino-acid sequence viewer.

MSGFKAGFLWGGAVAAHQLEGGWQEGGKGISVADVMTAGAHGVPREITDGVVAGKNYPNHEAIDFYHRYPQDLALFAEMGFKCFRTSIAWTRIFPQGDELEPNEAGLQFYDDLFDECLKHGIEPVITLSHFEMPYHLVTEYGGWRNRKLIDFFVRFARVVFTRYQHKVKYWMTFNEINNQANFHEDFAPFTNSGLKYLPDEDREPVMYQAAHYELVASALAVKAAREINPALQIGCMIAMCPIYPLTCAPDDMMMAMNAMHRRYWFTDVHVRGRYPQHLLNYFARRGFTLDITEADRQALTEGCVDYIGFSYYMSFATKATEDNPLLDYDETTSLVSNPYVKKSDWGWQIDPVGLRYSLNWFWDHYQLPLFIVENGFGAIDVREADGSVNDQYRIDYLSAHIAEMKKAVVEDGVDLMGYTPWGCIDLVSAGTGEMKKRYGFIYVDKDNEGNGTLARSRKKSFAWYQQVIASNGENLS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

3.2.1.86

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:0008706 Catalysis of the reaction: 6-phospho-beta-D-glucoside-(1,4)-D-glucose + H2O = D-glucose 6-phosphate + 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
370	378	ProSitePatterns	PS00572	Glycosyl hydrolases family 1 active site.
370	378	InterPro	IPR018120	Glycoside hydrolase family 1, active site
1	476	Gene3D	G3DSA:3.20.20.80	Glycosidases
2	469	SUPERFAMILY	SSF51445	(Trans)glycosidases
2	469	InterPro	IPR017853	Glycoside hydrolase superfamily
413	430	PRINTS	PR00131	Glycosyl hydrolase family 1 signature
413	430	InterPro	IPR001360	Glycoside hydrolase family 1
304	318	PRINTS	PR00131	Glycosyl hydrolase family 1 signature
304	318	InterPro	IPR001360	Glycoside hydrolase family 1
438	450	PRINTS	PR00131	Glycosyl hydrolase family 1 signature
438	450	InterPro	IPR001360	Glycoside hydrolase family 1
391	402	PRINTS	PR00131	Glycosyl hydrolase family 1 signature
391	402	InterPro	IPR001360	Glycoside hydrolase family 1
370	378	PRINTS	PR00131	Glycosyl hydrolase family 1 signature
370	378	InterPro	IPR001360	Glycoside hydrolase family 1
2	476	FunFam	G3DSA:3.20.20.80:FF:000004	Beta-glucosidase 6-phospho-beta-glucosidase
8	22	ProSitePatterns	PS00653	Glycosyl hydrolases family 1 N-terminal signature.
8	22	InterPro	IPR033132	Glycosyl hydrolases family 1, N-terminal conserved site
9	474	PANTHER	PTHR10353	GLYCOSYL HYDROLASE
9	474	InterPro	IPR001360	Glycoside hydrolase family 1
4	473	Pfam	PF00232	Glycosyl hydrolase family 1
4	473	InterPro	IPR001360	Glycoside hydrolase family 1

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 #2

0.78

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Surrounding area

Site 2 FPocket #1

0.415

Likely same site as P2Rank 1 2.4 Å 21 shared residues 84% of smaller site

Unusual size

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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

0.95

Likely same site as FPocket 1 2.4 Å 21 shared residues 84% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.627

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Surrounding area

Site 3 P2Rank #3

0.051

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Surrounding area

Site 4 P2Rank #4

0.021

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Surrounding area

Site 5 P2Rank #5

0.021

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Surrounding area

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #21

0.401

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Surrounding area

Site 2 FPocket #18

0.349

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Surrounding area

Site 3 FPocket #25

0.294

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Surrounding area

Site 4 FPocket #4

0.293

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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

0.957

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Surrounding area

Site 2 P2Rank #2

0.704

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Surrounding area

Site 3 P2Rank #3

0.077

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Surrounding area

Site 4 P2Rank #4

0.06

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Surrounding area

Site 5 P2Rank #5

0.026

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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_W9BC02	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_03814	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.

38 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 30 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

HBO PDB via homolog Detail RCSB PDB

IFM PDB via homolog Detail RCSB PDB

JAZ 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](…`
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`
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]…`

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL157924 ChEMBL	Q43014	6.96 ~109.6 nM	215.3 Da LogP 1.07 TPSA 60.9	✓ Ro5	✓ Clean	`NCCc1cn(C(=O)c2ccccc2)cn1`

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
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`
ZINC255989522 ZINC	0.593	276.2 Da LogP -2.39 TPSA 147.7	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1S[C@H](O)[C@H](O)[C@H](O)[C@@…`
ZINC255989523 ZINC	0.593	276.2 Da LogP -2.39 TPSA 147.7	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1S[C@H](O)[C@H](O)[C@H](O)[C@H…`
ZINC255989524 ZINC	0.593	276.2 Da LogP -2.39 TPSA 147.7	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1S[C@H](O)[C@H](O)[C@@H](O)[C@…`
ZINC39044667 ZINC	0.593	276.2 Da LogP -2.39 TPSA 147.7	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1S[C@@H](O)[C@H](O)[C@@H](O)[C@…`
ZINC44608494 ZINC	0.593	276.2 Da LogP -2.39 TPSA 147.7	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1S[C@H](O)[C@H](O)[C@@H](O)[C@…`
ZINC95864639 ZINC	0.593	276.2 Da LogP -2.39 TPSA 147.7	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1S[C@H](O)[C@H](O)[C@@H](O)[C@@…`
ZINC15442641 ZINC	0.550	353.5 Da LogP 4.22 TPSA 43.8	✓ Ro5	✓ Clean	`NCCc1cn(C(c2ccccc2)(c2ccccc2)c2ccccc2)cn1`
ZINC65734925 ZINC	0.548	211.3 Da LogP 1.17 TPSA 70.1	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)n1cnc(CCN)c1`
ZINC100351935 ZINC	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@…`
ZINC1529564 ZINC	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@@H](O)[C@H](O)[C@H](O)[C@…`
ZINC1532533 ZINC	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@H](O)[C@@H](O)[C@H](O)[C@…`
ZINC1532857 ZINC	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C…`
ZINC3581460 ZINC	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C…`
ZINC38276879 ZINC	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C@…`
ZINC38276880 ZINC	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@@H](O)[C@H](O)[C@H…`
ZINC3869397 ZINC	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C…`
ZINC3875374 ZINC	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C@…`
ZINC3875375 ZINC	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@…`
ZINC4095545 ZINC	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C@…`
ZINC4095546 ZINC	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@H…`
ZINC4096188 ZINC	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@@H](O)[C@@H](O)[C@…`
ZINC8551507 ZINC	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@H](O)[C@@H](O)[C@H](O)[C@…`
ZINC40641215 ZINC	0.512	201.3 Da LogP 1.43 TPSA 43.8	✓ Ro5	✓ Clean	`NCCc1cn(Cc2ccccc2)cn1`
ZINC12504154 ZINC	0.500	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@@H](O)[C@@H]1O`
ZINC1532546 ZINC	0.500	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@H](O)[C@@H](O)[C@H]1O`
ZINC4096190 ZINC	0.500	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@H](O)[C@@H]1O`
ZINC4228241 ZINC	0.500	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O`
ZINC4521831 ZINC	0.500	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@@H](O)[C@@H]1O`

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.