KpATCC43816 Protein target profile

beta-galactosidase

Accession: VK055_0887

Gene: AIK79510.1 lacZ 3D evidence: AlphaFold DB model + ColabFold model Metabolism 34 reactions UniProt A0A085DPL4
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Length 1035
Pocket druggability (P2Rank · AlphaFold DB model) 0.905
Metabolic reactions 34
Chokepoint No
Direct ligand evidence 0 67 total records
Functional annotation 1 EC 9 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

Central metabolic position More central than 95.4% of genes in this genome. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.91. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Low human similarity A human hit was flagged, but identity is only 23.516% - a weak match, lower risk than a close homolog. This target also has a predicted binding pocket (P2Rank 0.91) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 98 of 4744 screened genomes (2.1%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.91) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.74, 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 (%)
23.516 Lower values reduce human off-target concern.
Human E-value
1.03e-19
Gut microbiome similarity
2.1% 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
96.09 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) 0.905
Structure A0A085DPL4
Pocket Pocket 1
Druggability (FPocket) 0.744
Structure A0A085DPL4
Pocket Pocket 6
ColabFold model
P2Rank 0.92 · Pocket 1
FPocket 0.648 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 98 / 4744 genomes with a hit
Prevalence 2.1%

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 95.4% of genes in this genome.

Relative network centrality 95.4% more central than 95.4% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

Catalyzed reactions

34 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.

MQISDTGRSHTPDFHAVLAREDWQNQTITHLNRLPAHPVFASWRDELAARDNLPSSRRRQLDGEWQFSYARSPFAVDAQWLTQDLPDCRGTPVPSNWQMEGYDAPIYTNVRYPIDTTPPRVPEDNPTGCYSLHFTVEDTWRENGQTQIIFDGVNSAFHLWCNGVWVGYSQDSRLPAAFDLSPFLRPGDNRLCVMVMRWSAGSWLEDQDMWRMSGIFRSVWLLNKPQQRLCDVQLTPALDALYRDGTLQVQATVEATEAALAGLSVGVSLWRGEEQIAAGRQPLGTPTVDERGHYAERVDFSLAVATPAHWSAETPNCYRAVVTLWRGDELLEAEAWDIGFRRIEIADGLLRLNGKPLLIRGVNRHEHHHLRGQVVTEADMVQDILLMKQNNFNAVRCSHYPNAPRWYELCNRYGLYVVDEANIETHGMVPMNRLSDDPAWLPAFSARVTRMVQSNRNHPCIIIWSLGNESGGGGNHEALYHWLKRNDPSRPVQYEGGGADTTATDIICPMYARVERDQPIPAVPKWGIKKWISLPGEQRPLILCEYAHAMGNSLGNFADYWQAFREYPRLQGGFIWDWADQAIRKTFADGSVGWAYGGDFGDKPNDRQFCMNGLVFPDRTPHPSLVEAKHAQQYFQFTLLSTSPLRVRIISEYLFRPTDNEVLRWQVQAAGEPLYHGDLTLALPPEGSDEITLLDSLILPEGARAVWLTLEVTQPQATAWSEAEHRVAWQQFPLPAPLALPASTVSAGAPDLIVSDEAWQIRAGSQCWTIDRRTGLLSRWSVGGQEQLLTPLRDQFIRAPLDNDIGVSEVERIDPNAWVERWKSAGLYDLEAHCVQCDAQRLANETLVDCRWHYLRGEEVVIVSHWRMHFTADGTLRLAVDGERAETLPPLPRVGLHFQVADQQAPVSWLGLGPHENYPDRRSSACFARWEQPLAAMTTPYIFPTENGLRCDTQALDWGRWHISGHFHFSVQPWSTRQLMETDHWHKMQAEDGVWITLDGLHMGVGGDDSWTPSVLPQWLLSQTRWQYEVSLRCF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Subcellular localization

Localization
Unknown

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0030246 Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • 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:0004565 Catalysis of the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-D-galactosides.
  • GO:0009341 A protein complex that possesses beta-galactosidase activity, i.e. catalyzes the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. In E. coli, the complex is a homotetramer; dimeric and hexameric beta-galactosidase complexes have been observed in other species.
  • GO:0004553 Catalysis of the hydrolysis of any O-glycosyl bond.
  • GO:0016798 Catalysis of the hydrolysis of any glycosyl bond.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0005990 The chemical reactions and pathways resulting in the breakdown of lactose, the disaccharide galactopyranosyl-glucose.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

48 records
Show feature table
Start End DB Term Name
227 341 Gene3D G3DSA:2.60.40.10 Immunoglobulins
227 341 InterPro IPR013783 Immunoglobulin-like fold
17 1033 PANTHER PTHR46323 BETA-GALACTOSIDASE
629 738 SUPERFAMILY SSF49303 beta-Galactosidase/glucuronidase domain
629 738 InterPro IPR036156 Beta-Galactosidase/glucuronidase domain superfamily
342 632 FunFam G3DSA:3.20.20.80:FF:000018 Beta-galactosidase
59 225 Pfam PF02837 Glycosyl hydrolases family 2, sugar binding domain
59 225 InterPro IPR006104 Glycosyl hydrolases family 2, sugar binding domain
228 341 SUPERFAMILY SSF49303 beta-Galactosidase/glucuronidase domain
228 341 InterPro IPR036156 Beta-Galactosidase/glucuronidase domain superfamily
342 632 Gene3D G3DSA:3.20.20.80 Glycosidases
455 469 ProSitePatterns PS00608 Glycosyl hydrolases family 2 acid/base catalyst.
455 469 InterPro IPR023232 Glycoside hydrolase, family 2, active site
539 554 PRINTS PR00132 Glycosyl hydrolase family 2 signature
539 554 InterPro IPR006101 Glycoside hydrolase, family 2
352 366 PRINTS PR00132 Glycosyl hydrolase family 2 signature
352 366 InterPro IPR006101 Glycoside hydrolase, family 2
153 168 PRINTS PR00132 Glycosyl hydrolase family 2 signature
153 168 InterPro IPR006101 Glycoside hydrolase, family 2
455 470 PRINTS PR00132 Glycosyl hydrolase family 2 signature
455 470 InterPro IPR006101 Glycoside hydrolase, family 2
383 401 PRINTS PR00132 Glycosyl hydrolase family 2 signature
383 401 InterPro IPR006101 Glycoside hydrolase, family 2
766 1031 Pfam PF02929 Beta galactosidase small chain
766 1031 InterPro IPR004199 Beta galactosidase small chain/ domain 5
760 1033 SMART SM01038 Bgal_small_N_2
760 1033 InterPro IPR004199 Beta galactosidase small chain/ domain 5
343 632 SUPERFAMILY SSF51445 (Trans)glycosidases
343 632 InterPro IPR017853 Glycoside hydrolase superfamily
11 225 Gene3D G3DSA:2.60.120.260 -
12 1035 Hamap MF_01687 Beta-galactosidase [lacZ].
12 1035 InterPro IPR023933 Glycoside hydrolase, family 2, beta-galactosidase
633 741 Gene3D G3DSA:2.60.40.10 Immunoglobulins
633 741 InterPro IPR013783 Immunoglobulin-like fold
21 225 SUPERFAMILY SSF49785 Galactose-binding domain-like
21 225 InterPro IPR008979 Galactose-binding-like domain superfamily
393 418 ProSitePatterns PS00719 Glycosyl hydrolases family 2 signature 1.
393 418 InterPro IPR023230 Glycoside hydrolase, family 2, conserved site
647 735 Pfam PF16353 Beta-galactosidase, domain 4
647 735 InterPro IPR032312 Beta-galactosidase, domain 4
230 341 Pfam PF00703 Glycosyl hydrolases family 2
230 341 InterPro IPR006102 Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich
744 1034 Gene3D G3DSA:2.70.98.10 -
744 1034 InterPro IPR014718 Glycoside hydrolase-type carbohydrate-binding
343 636 Pfam PF02836 Glycosyl hydrolases family 2, TIM barrel domain
343 636 InterPro IPR006103 Glycoside hydrolase family 2, catalytic domain
745 1033 SUPERFAMILY SSF74650 Galactose mutarotase-like
745 1033 InterPro IPR011013 Galactose mutarotase-like domain superfamily

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
0.905
Likely same site as FPocket 10 1.5 Å 20 shared residues 83% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.728
Likely same site as FPocket 6 1.9 Å 33 shared residues 89% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.472
Likely same site as FPocket 1 5.2 Å 16 shared residues 94% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.464
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Surrounding area
Pocket 5 P2Rank #5
0.271
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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 #6
0.744 Unusual size
Likely same site as P2Rank 2 1.9 Å 33 shared residues 89% of smaller site
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Surrounding area
Pocket 2 FPocket #10
0.737 Unusual size
Likely same site as P2Rank 1 1.5 Å 20 shared residues 83% of smaller site
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Surrounding area
Pocket 3 FPocket #1
0.252 Unusual size
Likely same site as P2Rank 3 5.2 Å 16 shared residues 94% of smaller site
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Surrounding area
Pocket 4 FPocket #32
0.206
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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_A0A085DPL4
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_0887
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.

67 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 17 records from similar proteins
Structural ligands 11 0 loaded crystals
Measured bioactivity 6 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
149 PDB via homolog 178.1 Da · LogP -3.01 · TPSA 107.2 Open detail RCSB PDB
2DG PDB via homolog Detail RCSB PDB
BTB PDB via homolog Detail RCSB PDB
DGJ PDB via homolog Detail RCSB PDB
DVL 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
149 RCSB PDB
3CZJ
P00722 178.1 Da LogP -3.01 TPSA 107.2 ✓ Ro5 ✓ Clean C([C@@H]1[C@@H]([C@@H]([C@H](C(=O)O1)O)O)O)O
2DG RCSB PDB
4DUV
P00722 164.2 Da LogP -2.19 TPSA 90.2 ✓ Ro5 ✓ Clean C1[C@H]([C@H]([C@H](O[C@@H]1O)CO)O)O
BTB RCSB PDB
4DUV
P00722 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
DGJ RCSB PDB
6TSH
P00722 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
DVL RCSB PDB
6KUZ
P00722 537.6 Da LogP 2.84 TPSA 138.6 1 viol. ✓ Clean Cc1cc(c(c(c1)c2nc3ccccc3s2)OCc4ccc(cc4)O[C@H]5[…
F4X RCSB PDB
7BRS
P00722 568.7 Da LogP 3.38 TPSA 139.7 1 viol. ✓ Clean CC1(c2ccccc2[N+](=C1/C=C/c3ccc(cc3)O[C@H]4[C@@H…
F6L RCSB PDB
7BTK
P00722 560.6 Da LogP 2.85 TPSA 139.7 1 viol. ✓ Clean CC1(c2ccccc2[N+](=C1/C=C/c3ccc(cc3)O[C@H]4[C@@H…
GIF RCSB PDB
5T99
A0A2D0TCC8 147.2 Da LogP -2.08 TPSA 72.7 ✓ Ro5 ✓ Clean C1[C@@H]([C@@H]([C@@H](CN1)O)O)CO
GTZ RCSB PDB
1JZ6
P00722 202.2 Da LogP -3.02 TPSA 124.5 ✓ Ro5 ✓ Clean C([C@@H]1[C@@H]([C@@H]([C@H](c2n1nnn2)O)O)O)O
MLI RCSB PDB
6SE8
A0A023UGN9 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
PTQ RCSB PDB
5A1A
P00722 300.4 Da LogP -0.24 TPSA 90.2 ✓ Ro5 ✓ Clean c1ccc(cc1)CCS[C@H]2[C@@H]([C@H]([C@H]([C@H](O2)…

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 A0A085DPL4

Chemistry

ChEMBL SJ5 ChEMBL CHEMBL3770764 ChEMBL EVA ChEMBL CHEMBL3770736 ChEMBL CHEMBL593646 ChEMBL CHEMBL594698

Pathways

BioCyc RXN-19765 BioCyc RXN-19765-CPD-9116/WATER//P-NITROPHENOL/ALPHA-D-GALACTOSE/PROTON.55. BioCyc RXN-19765-CPD-9116/WATER//P-NITROPHENOL/GALACTOSE/PROTON.47. BioCyc RXN-24169[CCO-CYTOSOL]-CPD-9115/WATER//CPD-258/ALPHA-D-GALACTOSE/PROTON.62. BioCyc RXN-24169[CCO-CYTOSOL]-CPD-9115/WATER//CPD-258/D-galactopyranose/PROTON.62. BioCyc RXN-24169[CCO-CYTOSOL]-CPD-9115/WATER//CPD-258/GALACTOSE/PROTON.54. BioCyc RXN-24169[CCO-PERI-BAC]-CPD-9115/WATER//CPD-258/ALPHA-D-GALACTOSE/PROTON.63. BioCyc RXN-24169[CCO-PERI-BAC]-CPD-9115/WATER//CPD-258/D-galactopyranose/PROTON.63. BioCyc RXN-24169[CCO-PERI-BAC]-CPD-9115/WATER//CPD-258/GALACTOSE/PROTON.55. BioCyc RXN-25312 BioCyc RXN-25312-CPD-9117/WATER//PHENOL/ALPHA-D-GALACTOSE.41. BioCyc RXN-25312-CPD-9117/WATER//PHENOL/GALACTOSE.33. BioCyc RXN0-5363 BioCyc 3.2.1.23-RXN BioCyc 3.2.1.23-RXN-Beta-D-Galactosides/WATER//Non-Galactosylated-Galactose-Acceptors/ALPHA-D-GALACTOSE.84. BioCyc 3.2.1.23-RXN-Beta-D-Galactosides/WATER//Non-Galactosylated-Galactose-Acceptors/GALACTOSE.76. BioCyc BETAGALACTOSID-RXN[CCO-CYTOSOL]-CPD-15972/WATER//GALACTOSE/ALPHA-GLUCOSE.54. BioCyc BETAGALACTOSID-RXN[CCO-CYTOSOL]-CPD-15972/WATER//GALACTOSE/GLC.44. BioCyc BETAGALACTOSID-RXN[CCO-CYTOSOL]-CPD-15972/WATER//GALACTOSE/Glucopyranose.54. BioCyc BETAGALACTOSID-RXN[CCO-PERI-BAC]-CPD-15972/WATER//GALACTOSE/ALPHA-GLUCOSE.55. BioCyc BETAGALACTOSID-RXN[CCO-PERI-BAC]-CPD-15972/WATER//GALACTOSE/GLC.45. BioCyc BETAGALACTOSID-RXN[CCO-PERI-BAC]-CPD-15972/WATER//GALACTOSE/Glucopyranose.55. BioCyc RXN-12398 BioCyc RXN-12398-CPD-13376/WATER//CPD-13375/ALPHA-D-GALACTOSE.45. BioCyc RXN-12398-CPD-13376/WATER//CPD-13375/GALACTOSE.37. BioCyc RXN-12399 BioCyc RXN-12399-CPD-13377/WATER//CPD-13375/ALPHA-D-GALACTOSE.45. BioCyc RXN-12399-CPD-13377/WATER//CPD-13375/GALACTOSE.37. BioCyc RXN-12400 BioCyc RXN-12400-CPD-13378/WATER//CPD-13375/ALPHA-D-GALACTOSE.45. BioCyc RXN-12400-CPD-13378/WATER//CPD-13375/GALACTOSE.37. BioCyc RXN-17726 BioCyc RXN-17726-CPD-3561/WATER//GALACTOSE/BETA-D-FRUCTOSE.42. BioCyc RXN-17726-CPD-3561/WATER//GALACTOSE/CPD-10723.36.