KpKP13 Protein target profile

Biofilm PGA synthesis N-glycosyltransferase pgaC

Accession: KP13_00472

Gene: AHE46794.1 pgaC 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GH44
Length 442
Pocket druggability (P2Rank · AlphaFold DB model) 0.993
Direct ligand evidence 0 56 total records
Functional annotation 1 EC 3 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
Hit
Human identity (%)
32.0 Lower values reduce human off-target concern.
Human E-value
2.78e-08
Gut microbiome similarity
1.6% 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
89.47 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) 0.993
Structure A0A0H3GH44
Pocket Pocket 1
Druggability (FPocket) 0.966
Structure A0A0H3GH44
Pocket Pocket 19
ColabFold model
P2Rank 0.99 · Pocket 1
FPocket 0.698 · Pocket 33
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 74 / 4744 genomes with a hit
Prevalence 1.6%

Sequence

Primary amino-acid sequence viewer.

MTDRIIALCILCLVFGLPLGVAAVFTGELILDFVFFWPLFMSVLWITGGLYFWFQLERHWPWGEDTPPPTLPGNPLISILIPCFNEEKNARETISAALAQRYANLEVIAINDGSSDNTAQVLQQLAQEEPRLRVIHLAANQGKAVALKAGAAAARGDLLVCIDGDALLDRDTAAWLVAPLIHYPHVGAVTGNPRIRTRSTLIGRIQVGEFSSIIGLIKRTQRIYGRVFTVSGVIAAFRRQALADVGYWSPDMITEDIDISWKLQLRHWDIFFEPRALCWILMPETLKGLWKQRLRWAQGGAEVFLVNLRRLFHWQHHRMWPLFLEYACSTLWAFAYAITILLFILSRLIPLPDNLAVHSLFPPEFTGMLLGLMCLLQFVASLYIERRYEKKVAKSLFWVIWFPMVYWMIGLLTTLVAFPKVMVKRQRSRARWVSPDRGKGSL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Subcellular localization

Localization
CytoplasmicMembrane

Enzyme Commission (EC)

1

Gene Ontology (GO)

3
  • GO:0043708 The attachment of a cell to a solid substrate, via cell adhesion molecules, contributing to the formation of a biofilm.
  • GO:0008375 Catalysis of the transfer of an N-acetylglucosaminyl residue from UDP-N-acetyl-glucosamine to a sugar.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
365 384 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
323 345 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
5 27 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
55 318 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 23 Phobius SIGNAL_PEPTIDE Signal peptide region
5 15 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
396 418 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
79 256 CDD cd06423 CESA_like
62 341 SUPERFAMILY SSF53448 Nucleotide-diphospho-sugar transferases
62 341 InterPro IPR029044 Nucleotide-diphospho-sugar transferases
346 364 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
24 32 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
396 418 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
70 287 Gene3D G3DSA:3.90.550.10 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
70 287 InterPro IPR029044 Nucleotide-diphospho-sugar transferases
419 442 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
365 384 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
33 54 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
319 345 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
16 23 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
73 439 PANTHER PTHR43630 POLY-BETA-1,6-N-ACETYL-D-GLUCOSAMINE SYNTHASE
77 298 Pfam PF13641 Glycosyltransferase like family 2
385 395 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
32 54 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
31 438 NCBIfam TIGR03937 poly-beta-1,6-N-acetyl-D-glucosamine synthase
31 438 InterPro IPR023853 Poly-beta-1,6 N-acetyl-D-glucosamine synthase PgaC/IcaA
1 4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.

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
0.993
Likely same site as FPocket 19 4.5 Å 29 shared residues 94% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.546
Likely same site as FPocket 30 1.0 Å 15 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.457
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Surrounding area
Pocket 4 P2Rank #4
0.304
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Surrounding area
Pocket 5 P2Rank #5
0.094
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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 #19
0.966 Unusual size
Likely same site as P2Rank 1 4.5 Å 29 shared residues 94% of smaller site
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Surrounding area
Pocket 2 FPocket #1
0.65
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Surrounding area
Pocket 3 FPocket #30
0.645
Likely same site as P2Rank 2 1.0 Å 15 shared residues 100% of smaller site
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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_A0A0H3GH44
AlphaFold DB full sequence Viewing
ColabFold KP13_00472
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.

56 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 6 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 1 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
GDD PDB via homolog 605.3 Da · LogP -4.63 · TPSA 331.7 Open detail RCSB PDB
LDA PDB via homolog Detail RCSB PDB
MJC PDB via homolog Detail RCSB PDB
UD2 PDB via homolog Detail RCSB PDB
UGA 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
GDD RCSB PDB A3MTD6 605.3 Da LogP -4.63 TPSA 331.7 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
LDA RCSB PDB Q8U4M3 229.4 Da LogP 4.48 TPSA 23.1 ✓ Ro5 ✓ Clean CCCCCCCCCCCC[N+](C)(C)[O-]
MJC RCSB PDB Q8U4M3 1011.5 Da LogP 16.23 TPSA 145.9 2 viol. ✓ Clean C[C@H](CCC=C(C)CCC=C(C)CC/C=C(\C)/CC/C=C(\C)/CC…
UD2 RCSB PDB Q8L0V4 607.4 Da LogP -4.65 TPSA 305.9 3 viol. ✓ Clean CC(=O)N[C@@H]1[C@H]([C@H]([C@H](O[C@@H]1O[P@@](…
UGA RCSB PDB Q8L0V4 580.3 Da LogP -4.70 TPSA 314.1 3 viol. ✓ Clean C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…

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.