KpKP13 Protein target profile

Alpha-galactosidase

Accession: KP13_00463

Gene: AHE46803.1 melA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GL60
Length 450
Pocket druggability (P2Rank · AlphaFold DB model) 0.942
Direct ligand evidence 0 52 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.

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
1.2% 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
95.75 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) 0.942
Structure A0A0H3GL60
Pocket Pocket 1
Druggability (FPocket) 0.331
Structure A0A0H3GL60
Pocket Pocket 22
ColabFold model
P2Rank 0.964 · Pocket 1
FPocket 0.143 · Pocket 24
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 56 / 4744 genomes with a hit
Prevalence 1.2%

Sequence

Primary amino-acid sequence viewer.

MSAPKITFIGAGSTVFVKNILGDVFQRPALKSAHIALMDIDETRLEESHIVVRKLMDSVGANGEISCHRDRKTALQGANFVVVAFQIGGYEPCTVTDFAVCKRHGLEQTIADTLGPGGIMRALRTIPHLWAICDDMSEVCPDATMLNYVNPMAMNTWAMYARYPHIKQVGLCHSVQGTAEELARDLDLDPADLRYRCAGINHMAFYLSLEKKLADGSYVSIYPDLLQAYADGRAPKPNLHGNPRCENIVRYEMLKKLGYFVTESSEHFAEYTPWFIKPGRDDLLARYKVPLDEYPKRCVEQLANWHQELESYKRGERIEVKPSREYASTIMNAIWTGEPSVVYGNVRNDNLIDNLPQGCCVEVACLVDANGIQPTKVGALPAHLAALMQTNINVQTLLTEAILTENRDYVYYATMMDPHTAAVLGIEEIYALVDDLIASHGDWLPAWLHR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Subcellular localization

Localization
Cytoplasmic

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: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:0016616 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
  • GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
141 172 ProSitePatterns PS01324 Glycosyl hydrolases family 4 signature.
141 172 InterPro IPR019802 Glycoside hydrolase, family 4, conserved site
4 170 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
4 170 InterPro IPR036291 NAD(P)-binding domain superfamily
1 444 Gene3D G3DSA:3.90.1820.10 -
4 437 CDD cd05297 GH4_alpha_glucosidase_galactosidase
112 132 PRINTS PR00732 Glycosyl hydrolase family 4 signature
112 132 InterPro IPR001088 Glycoside hydrolase, family 4
167 178 PRINTS PR00732 Glycosyl hydrolase family 4 signature
167 178 InterPro IPR001088 Glycoside hydrolase, family 4
193 205 PRINTS PR00732 Glycosyl hydrolase family 4 signature
193 205 InterPro IPR001088 Glycoside hydrolase, family 4
74 90 PRINTS PR00732 Glycosyl hydrolase family 4 signature
74 90 InterPro IPR001088 Glycoside hydrolase, family 4
5 20 PRINTS PR00732 Glycosyl hydrolase family 4 signature
5 20 InterPro IPR001088 Glycoside hydrolase, family 4
96 109 PRINTS PR00732 Glycosyl hydrolase family 4 signature
96 109 InterPro IPR001088 Glycoside hydrolase, family 4
141 158 PRINTS PR00732 Glycosyl hydrolase family 4 signature
141 158 InterPro IPR001088 Glycoside hydrolase, family 4
5 187 Pfam PF02056 Family 4 glycosyl hydrolase
5 187 InterPro IPR001088 Glycoside hydrolase, family 4
173 448 SUPERFAMILY SSF56327 LDH C-terminal domain-like
173 448 InterPro IPR015955 Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal
1 448 PANTHER PTHR32092 6-PHOSPHO-BETA-GLUCOSIDASE-RELATED
1 448 InterPro IPR001088 Glycoside hydrolase, family 4
197 420 Pfam PF11975 Family 4 glycosyl hydrolase C-terminal domain
197 420 InterPro IPR022616 Glycosyl hydrolase, family 4, C-terminal

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

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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
0.942
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.322
Likely same site as FPocket 22 1.8 Å 12 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.061
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.046
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #22
0.331 Unusual size
Likely same site as P2Rank 2 1.8 Å 12 shared residues 100% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:150-150
UniProt: Binding site:172-172
UniProt: Binding site:202-202
UniProt: Site:112-112 Increases basicity of active site Tyr
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_A0A0H3GL60
AlphaFold DB full sequence Viewing
ColabFold KP13_00463
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.

52 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 2 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
G6P PDB via homolog 260.1 Da · LogP -3.10 · TPSA 156.9 Open detail RCSB PDB
LMR PDB via homolog Detail RCSB PDB
ZINC100351935 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC1529564 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC1532533 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

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
G6P RCSB PDB P54716 260.1 Da LogP -3.10 TPSA 156.9 1 viol. ✓ Clean C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)OP…
LMR RCSB PDB Q9AGA6 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)O)C(=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.

Cross-references

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