KpATCC43816 Protein target profile

glycogen debranching enzyme GlgX

Accession: VK055_3674

Gene: AIK82229.1 glgX 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GYH9
Length 658
Pocket druggability (P2Rank · AlphaFold DB model) 0.871
Direct ligand evidence 0 54 total records
Functional annotation 1 EC 7 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
2.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
45.122 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
97.46 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) 0.871
Structure A0A0H3GYH9
Pocket Pocket 1
Druggability (FPocket) 0.651
Structure A0A0H3GYH9
Pocket Pocket 8
ColabFold model
P2Rank 0.922 · Pocket 1
FPocket 0.604 · Pocket 4
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 131 / 4744 genomes with a hit
Prevalence 2.8%

Metabolic context

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

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MTSLAAGKPAPLGASYDGKGVNFALFSAHAERVELCVFDEQGNEQRFDLPARSGDIWHGWLAAAGPGLRYGYRVHGPWDPAQGHRFNPAKLLIDPSAHRVEGDLPDDERLHGGMWQPDRRDSAAVAPKSQVVDLRYDWRGDKPPRTPWGETVIYEAHVKGLTLLNPQLPEAIRGTYKALGHPAMIAYFKSLGISALELLPVAQFASEPRLQRMGLSNYWGYNPLAWFALDPRYASDPDRALDEFRDAVKALHAAGIEVILDIVLNHSAEIDLEGPTVSLRGIDNRSYYWVREDGDYHNWTGCGNTLNLSHPGVVEWARQCLRFWVDECHVDGFRFDLASVMGRTPEFRQDAPLFEAIRRDSVLSQVKLIAEPWDIGPGGYQVGNFPPLFAEWNDHFRDSARRFWLQQNVSLGDFAQRFAASSDLFARDGKPPSATVNLVTAHDGFTLRDCVCFNQKHNEANGEENRDGTNNNYSNNHGIEGLEANFAVIERRRASAHALLTTLLLAQGTPMLLAGDEQGHSQHGNNNAYCQDNALTWLDWRQANPGLTAFTAALIHLRRRIPALTRNRWWQEGDGNVRWLNRNAQPLTAAEWQQGAACMQIQLSDRWLLTLNATAEVVDMVLPEGEWRAVPPFAGEDNPVIMAVWHGPAHGVCVFQRS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • 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:0004133 OBSOLETE. Catalysis of the cleavage of branch points in branched glycogen polymers.
  • GO:0005977 The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages.
  • GO:0005980 The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.
  • GO:0004553 Catalysis of the hydrolysis of any O-glycosyl bond.
  • GO:0004135 Catalysis of the hydrolysis of (1->6)-alpha-D-glucosidic branch linkages in glycogen phosphorylase limit dextrin. Limit dextrin is the highly branched core that remains after exhaustive treatment of glycogen with glycogen phosphorylase. It is formed because these enzymes cannot hydrolyze the (1->6) glycosidic linkages present.
  • GO:0120549 Catalysis of the hydrolysis of (1->6)-alpha-D-glucosidic linkages to branches with degrees of polymerization of three or four glucose residues in limit dextrin.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
130 558 SMART SM00642 aamy
130 558 InterPro IPR006047 Glycosyl hydrolase, family 13, catalytic domain
135 565 SUPERFAMILY SSF51445 (Trans)glycosidases
135 565 InterPro IPR017853 Glycoside hydrolase superfamily
571 655 Pfam PF18390 Glycogen debranching enzyme C-terminal domain
571 655 InterPro IPR040784 Glycogen debranching enzyme, C-terminal domain
135 572 Gene3D G3DSA:3.20.20.80 Glycosidases
3 657 Hamap MF_01248 Glycogen debranching enzyme [glgX].
3 657 InterPro IPR022844 Glycogen debranching enzyme, bacterial
11 96 Pfam PF02922 Carbohydrate-binding module 48 (Isoamylase N-terminal domain)
11 96 InterPro IPR004193 Glycoside hydrolase, family 13, N-terminal
185 287 Pfam PF00128 Alpha amylase, catalytic domain
185 287 InterPro IPR006047 Glycosyl hydrolase, family 13, catalytic domain
7 634 NCBIfam TIGR02100 glycogen debranching protein GlgX
7 634 InterPro IPR011837 Glycogen debranching enzyme, GlgX type
1 133 Gene3D G3DSA:2.60.40.10 Immunoglobulins
1 133 InterPro IPR013783 Immunoglobulin-like fold
4 626 PANTHER PTHR43002 GLYCOGEN DEBRANCHING ENZYME
573 657 Gene3D G3DSA:2.60.40.1180 -
573 657 InterPro IPR013780 Glycosyl hydrolase, all-beta
136 561 CDD cd11326 AmyAc_Glg_debranch
11 133 CDD cd02856 E_set_GDE_Isoamylase_N
11 133 InterPro IPR044505 Glycogen debranching enzyme GlgX/isoamylase, N-terminal Early set domain
7 144 SUPERFAMILY SSF81296 E set domains
7 144 InterPro IPR014756 Immunoglobulin E-set

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
0.871
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Surrounding area
Pocket 2 P2Rank #2
0.389
Likely same site as FPocket 8 2.2 Å 15 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.26
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Surrounding area
Pocket 4 P2Rank #4
0.207
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Surrounding area
Pocket 5 P2Rank #5
0.125
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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 #8
0.651 Unusual size
Likely same site as P2Rank 2 2.2 Å 15 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #7
0.583
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Surrounding area
Residue sets
UniProt: Active site:336-336 Nucleophile
UniProt: Active site:371-371 Proton donor
UniProt: Site:443-443 Transition state stabilizer
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_A0A0H3GYH9
AlphaFold DB full sequence Viewing
ColabFold VK055_3674
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.

54 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 4 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ARE PDB via homolog 807.7 Da · LogP -10.74 · TPSA 400.3 Open detail RCSB PDB
BTB PDB via homolog Detail RCSB PDB
FLC PDB via homolog Detail RCSB PDB
TAM PDB via homolog Detail RCSB PDB
ZINC1615342 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
ARE RCSB PDB Q08751 807.7 Da LogP -10.74 TPSA 400.3 3 viol. ✓ Clean C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@…
BTB RCSB PDB Q8ZPF0 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
FLC RCSB PDB Q55088 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
TAM RCSB PDB A0A0C5GWS2 163.2 Da LogP -1.17 TPSA 86.7 ✓ Ro5 ✓ Clean C(CO)C(CCO)(CCO)N

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.