KpATCC43816 Protein target profile

phosphopantothenoylcysteine decarboxylase / phosphopantothenate--cysteine ligase

Accession: VK055_3490

Gene: AIK82046.1 coaBC 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GUS9
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Length 405
Pocket druggability (P2Rank · AlphaFold DB model) 0.868
Metabolic reactions 1
Chokepoint Yes
Direct ligand evidence 0 53 total records
Functional annotation 0 EC 8 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

Metabolic chokepoint Catalyzes a reaction that is the only producer or consumer of a metabolite in the imported metabolic model. Central metabolic position More central than 93.7% of genes in this genome. No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. Second pocket predictor agrees P2Rank predicted binding-site probability 0.87. Review the complete evidence below

Risks to review

Human similarity Top human hit identity: 32.571%. This target also has a predicted binding pocket (P2Rank 0.87) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 176 of 4744 screened genomes (3.7%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.87) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant. Best pocket may be a modeling artifact FPocket selected-pocket score 0.70, 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 (%)
32.571 Lower values reduce human off-target concern.
Human E-value
1.22e-17
Gut microbiome similarity
3.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
93.46 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) 0.868
Structure A0A0H3GUS9
Pocket Pocket 1
Druggability (FPocket) 0.698
Structure A0A0H3GUS9
Pocket Pocket 17
ColabFold model
P2Rank 0.744 · Pocket 1
FPocket 0.829 · Pocket 6
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 176 / 4744 genomes with a hit
Prevalence 3.7%

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a consuming chokepoint reaction in Pantothenate and CoA biosynthesis, no isoenzyme backup detected, more central than 93.7% of genes in this genome.

Relative network centrality 93.7% more central than 93.7% of genes in this genome
Chokepoint Chokepoint gene
Pathways
Pantothenate and CoA biosynthesis
Catalyzed reaction

1 reaction 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.

MMTLAGKKIVLGVSGGIAAYKTPELVRRLRERGAEVRVAMTEAAKAFITPLSLQAVSGYPVSDSLLDPAAEAAMGHIELGKWADLVILAPATADLIARVAAGMANDLVSTICLATPSPVAVVPAMNQQMYRAQATQHNLQTLATRGLLLWGPDSGSQACGDVGPGRMLDPLTIVDMAAQHFASPVKDLQHLNLMITAGPTREPLDPVRYITNHSSGKMGFAIAAAAAQRGANVTLISGPVSLPTPPFVQRIDVTTALEMEAAVQAGAQQQHIFIGCAAVADYRAAVIAEDKIKKQGDELTIKMVKNPDIVAGVAALKSHRPYVVGFAAETNNVEEYARQKRARKNLDLICANDVSQPNQGFNSDSNALHLFWQDGEKRLPLERKELLGQLLLDEIVTRYDEKNRR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

8
  • 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:0015941 The chemical reactions and pathways resulting in the breakdown of pantothenate, the anion of pantothenic acid. It is a B complex vitamin that is a constituent of coenzyme A and is distributed ubiquitously in foods.
  • GO:0004632 Catalysis of the reaction: CTP + (R)-4'-phosphopantothenate + L-cysteine = CMP + diphosphate + (R)-4'-phosphopantothenoyl-L-cysteine. Cysteine can be replaced by some of its derivatives.
  • GO:0004633 Catalysis of the reaction: N-[(R)-4-phosphonatopantothenoyl]-L-cysteinate + H+ = CO2 + pantetheine 4'-phosphate.
  • GO:0010181 Binding to flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
  • GO:0015937 The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester.
  • GO:0071513 A protein complex that catalyzes decarboxylation of 4'-phosphopantothenoylcysteine to yield 4'-phosphopantetheine; this is the third step in the biosynthesis of Coenzyme A. The complex is homotrimeric in many eukaryotes, but is a heterotrimer in Saccharomyces.
  • GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
187 405 FunFam G3DSA:3.40.50.10300:FF:000001 Coenzyme A biosynthesis bifunctional protein CoaBC
186 400 SUPERFAMILY SSF102645 CoaB-like
186 400 InterPro IPR035929 CoaB-like superfamily
1 186 Gene3D G3DSA:3.40.50.1950 -
1 186 InterPro IPR036551 Flavin prenyltransferase-like
1 186 FunFam G3DSA:3.40.50.1950:FF:000002 Coenzyme A biosynthesis bifunctional protein CoaBC
7 398 Hamap MF_02225 Coenzyme A biosynthesis bifunctional protein CoaBC [coaBC].
7 398 InterPro IPR005252 Coenzyme A biosynthesis bifunctional protein CoaBC
189 370 Pfam PF04127 DNA / pantothenate metabolism flavoprotein
189 370 InterPro IPR007085 DNA/pantothenate metabolism flavoprotein, C-terminal
4 396 NCBIfam TIGR00521 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase CoaBC
4 396 InterPro IPR005252 Coenzyme A biosynthesis bifunctional protein CoaBC
7 180 Pfam PF02441 Flavoprotein
7 180 InterPro IPR003382 Flavoprotein
187 405 Gene3D G3DSA:3.40.50.10300 -
187 405 InterPro IPR035929 CoaB-like superfamily
6 262 PANTHER PTHR14359 HOMO-OLIGOMERIC FLAVIN CONTAINING CYS DECARBOXYLASE FAMILY
3 181 SUPERFAMILY SSF52507 Homo-oligomeric flavin-containing Cys decarboxylases, HFCD
3 181 InterPro IPR036551 Flavin prenyltransferase-like

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
0.868
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Surrounding area
Pocket 2 P2Rank #2
0.244
Likely same site as FPocket 17 1.2 Å 17 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.078
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Surrounding area
Pocket 4 P2Rank #4
0.032
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Surrounding area
Pocket 5 P2Rank #5
0.02
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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 #17
0.698 Unusual size
Likely same site as P2Rank 2 1.2 Å 17 shared residues 100% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:159-159 Proton donor
UniProt: Binding site:275-277
UniProt: Binding site:281-281
UniProt: Binding site:291-291
UniProt: Binding site:307-310
UniProt: Binding site:326-326
UniProt: Binding site:340-340
UniProt: Binding site:344-344
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_A0A0H3GUS9
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_3490
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.

53 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 3 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
N9N PDB via homolog 246.2 Da · LogP 1.74 · TPSA 98.0 Open detail RCSB PDB
PCO PDB via homolog Detail RCSB PDB
PMT PDB via homolog Detail RCSB PDB
ZINC507420 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC225866 ZINC proposed compound · Tanimoto 0.714 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
N9N RCSB PDB
6THC
A0QWT2 246.2 Da LogP 1.74 TPSA 98.0 ✓ Ro5 Alert c1cc(ccc1C(=O)c2ccc(c(c2O)O)O)O
PCO RCSB PDB
1MVN
Q9SWE5 276.4 Da LogP -0.61 TPSA 98.7 ✓ Ro5 ✓ Clean CC(C)(CO)[C@H](C(=O)NCCC(=O)N\C=C/S)O
PMT RCSB PDB
1U7Z
P0ABQ0 604.4 Da LogP -2.89 TPSA 299.5 3 viol. ✓ Clean CC(C)(COP(=O)(O)O)[C@H](C(=O)NCCC(=O)O[P@@](=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.

Sequence

UniProt A0A0H3GUS9

Pathways

KEGG R03269 BioCyc P-PANTOCYSDECARB-RXN