KpKP13 Protein target profile

Beta-hexosaminidase

Accession: KP13_31490

Gene: AHE45266.1 nagZ 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GRI5
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Length 340
Pocket druggability (P2Rank · AlphaFold DB model) 0.88
Direct ligand evidence 0 61 total records
Functional annotation 1 EC 9 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.

Main supporting evidence

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.88, FPocket 0.74). Use the 3D pocket comparison to verify whether they identify the same site. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.74. This is a computational pocket signal, not binding validation. Review the complete evidence below

Risks to review

Microbiome similarity 141 of 4744 screened genomes (3.0%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.88) — check the ligand evidence before deprioritizing on off-target risk alone.

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
No hit
Gut microbiome similarity
3.0% 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
95.86 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) 0.88
Structure A0A0H3GRI5
Pocket Pocket 1
Druggability (FPocket) 0.744
Structure A0A0H3GRI5
Pocket Pocket 2
ColabFold model
P2Rank 0.893 · Pocket 1
FPocket 0.355 · Pocket 4
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 141 / 4744 genomes with a hit
Prevalence 3.0%

Sequence

Primary amino-acid sequence viewer.

MGPVMLDVEGYELDAEEREILAHPLVGGLILFTRNYHDPAQLRELVRQIRDASRNHLVVAVDQEGGRVQRFREGFTRLPAAQSFAALLGMEEGGKLAAEAGWLMASEMIAMDIDISFAPVLDVGHISAAIGERSYHEDPQKALTMARHFIDGMHAAGMKTTGKHFPGHGAVTADSHKETPFDPRAASVIRDHDMAVFKSLIAEQRLDAIMPAHVIYPELDPRPASGSAYWLKTVLRGELGFDGVIFSDDLSMEGAAIMGSYAERGQASLDAGCDMILVCNNRKGAVSVLDNLSPIKAERVTKLYHKGSFSRQELRDSARWKTVSAQLEQLHARWQEAKSA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • 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:0004563 Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0051301 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
  • GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
  • GO:0009252 The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.
  • GO:0009254 The continual breakdown and regeneration of peptidoglycan required to maintain the bacterial cell wall. Peptidoglycans consist of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.
  • GO:0008360 Any process that modulates the surface configuration of a cell.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
2 319 SUPERFAMILY SSF51445 (Trans)glycosidases
2 319 InterPro IPR017853 Glycoside hydrolase superfamily
1 337 FunFam G3DSA:3.20.20.300:FF:000001 Beta-hexosaminidase
1 340 Gene3D G3DSA:3.20.20.300 -
1 340 InterPro IPR036962 Glycoside hydrolase, family 3, N-terminal domain superfamily
234 251 ProSitePatterns PS00775 Glycosyl hydrolases family 3 active site.
234 251 InterPro IPR019800 Glycoside hydrolase, family 3, active site
3 332 Hamap MF_00364 Beta-hexosaminidase [nagZ].
3 332 InterPro IPR022956 Beta-hexosaminidase, bacterial
9 300 Pfam PF00933 Glycosyl hydrolase family 3 N terminal domain
9 300 InterPro IPR001764 Glycoside hydrolase, family 3, N-terminal
3 319 PANTHER PTHR30480 BETA-HEXOSAMINIDASE-RELATED

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
0.88
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Surrounding area
Pocket 2 P2Rank #2
0.323
Likely same site as FPocket 2 1.1 Å 13 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.303
Likely same site as FPocket 1 2.3 Å 19 shared residues 100% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.105
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Surrounding area
Pocket 5 P2Rank #5
0.032
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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 #2
0.744
Likely same site as P2Rank 2 1.1 Å 13 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #1
0.48 Unusual size
Likely same site as P2Rank 3 2.3 Å 19 shared residues 100% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:172-172 Proton donor/acceptor
UniProt: Active site:244-244 Nucleophile
UniProt: Binding site:129-129
UniProt: Binding site:159-160
UniProt: Binding site:58-58
UniProt: Binding site:66-66
UniProt: Site:170-170 Important for catalytic activity
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_A0A0H3GRI5
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_31490
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.

61 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 11 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 4 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
1BW PDB via homolog 232.3 Da · LogP -2.04 · TPSA 101.8 Open detail RCSB PDB
C76 PDB via homolog Detail RCSB PDB
H9J PDB via homolog Detail RCSB PDB
NOK PDB via homolog Detail RCSB PDB
NP6 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
1BW RCSB PDB
4HZM
Q8ZQ06 232.3 Da LogP -2.04 TPSA 101.8 ✓ Ro5 ✓ Clean CCCC(=O)N[C@H]1CN[C@@H]([C@H]([C@@H]1O)O)CO
C76 RCSB PDB
6JTK
Q5FA94 275.2 Da LogP -2.54 TPSA 119.3 ✓ Ro5 ✓ Clean C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)NC(=O)C…
H9J RCSB PDB
6DTE
A0A125HFC0 289.2 Da LogP -2.90 TPSA 130.2 1 viol. ✓ Clean C(C1[C@H]([C@@H](C([C@H]([C@@H]1O)O)NC(=O)C(F)(…
NOK RCSB PDB
5G5K
Q9HZK0 204.2 Da LogP -2.82 TPSA 101.8 ✓ Ro5 ✓ Clean CC(=O)N[C@H]1CN[C@@H]([C@H]([C@@H]1O)O)CO
NP6 RCSB PDB
3GS6
Q9KU37 381.4 Da LogP -0.05 TPSA 149.7 ✓ Ro5 ✓ Clean CCCC(=O)N[C@@H]\1[C@H]([C@@H]([C@H](O/C1=N\OC(=…
OAN RCSB PDB
2OXN
Q9KU37 353.3 Da LogP -0.83 TPSA 149.7 ✓ Ro5 ✓ Clean CC(=O)N[C@@H]\1[C@H]([C@@H]([C@H](O/C1=N\OC(=O)…
VPU RCSB PDB
3GSM
Q9KU37 395.4 Da LogP 0.34 TPSA 149.7 ✓ Ro5 ✓ Clean CCCCC(=O)N[C@@H]\1[C@H]([C@@H]([C@H](O/C1=N\OC(…

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.

Cross-references

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

Sequence

UniProt A0A0H3GRI5

Chemistry

ChEMBL CHEMBL2047302 ChEMBL CHEMBL2047303 ChEMBL CHEMBL2047304 ChEMBL CHEMBL2047305