Protein target profile

VK055_3231

ppc

Genome: KpATCC43816 Gene: AIK81792.1 ppc 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GK93
Length 883
Pocket druggability 0.957
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 54 total records
Functional annotation 1 EC 7 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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
3.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
93.97 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.957
Structure A0A0H3GK93
Pocket Pocket 1
P2Rank 0.88
Structure A0A0H3GK93
Pocket Pocket 1
ColabFold model
FPocket 0.801 · Pocket 1
P2Rank 0.901 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 164 / 4744 genomes with a hit
Prevalence 3.5%

Cross-references

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

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 97.8% of genes in this genome, no human homolog detected.

Relative network centrality 97.8% more central than 97.8% of genes in this genome
Chokepoint Not a chokepoint
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.

MNEQYSALRSNVSMLGKVLGDTIKDALGENILDRVETIRKLSKSSRAGNEANRQELLTTLQNLSNDELLPVARAFSQFLNLANTAEQYHSISANGEAASNPEVIARTLRKLKDQPNLNEETIKQAVESLSLELVLTAHPTEITRRTLIHKMVEVNNCLKQLDNKDIADYEHHQLMRRLRQLIAQSWHTDEIRKHRPSPVDEAKWGFAVVENSLWEGVPNYLRELNEQLEANLGYQLPVDFVPVRFTSWMGGDRDGNPNVTADITRHVLLLSRWKATDLFLKDVQVLISELSMVECTDELRALAGAEGAQEPYRYLMKKLRSQLMETQAWLEARLKGQKLPKPAGLITQNEQLWEPLYACYKSLQACGMGIIANGELLDTLRRVKSFGVPLVRIDIRQESTRHTEALGEMTRYLGIGDYESWSEADKQAFLIRELNSKRPLLPRQWEPSEETREVLDTCKVIAEAPRGSIAAYVISMAKTPSDVLAVHLLLKEAGIGFALPVAPLFETLDDLNNANDVMTQLLNIDWYRGFIQGKQMVMIGYSDSAKDAGVMAASWAQYQAQDALIKTCEKAGIELTLFHGRGGSIGRGGAPAHAALLSQPPGSLKGGLRVTEQGEMIRFKYGLPEVTISSLSLYTSAILEANLLPPPEPKAEWRDIMAELSDVSCKMYRGYVRENKDFVPYFRSATPEQELGKLPLGSRPAKRRPTGGVESLRAIPWIFAWTQNRLMLPAWLGAGAALQKVVEGGKQSELEAMCRDWPFFSTRLGMLEMVYSKADLWLAEYYDQRLVKPELWALGSELRKLLAADINVVLAIANDSHLMADLPWIAESIQLRNIYTDPLNVLQAELLHRSRQAEEEGKDPDPRVEQALMVTIAGVAAGMRNTG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0006099 A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
  • 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:0015977 A metabolic process in which carbon (usually derived from carbon dioxide) is incorporated into organic compounds (usually carbohydrates).
  • GO:0008964 Catalysis of the reaction: phosphate + oxaloacetate = phosphoenolpyruvate + HCO3-.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0006107 The chemical reactions and pathways involving oxaloacetate, the anion of oxobutanedioic acid, an important intermediate in metabolism, especially as a component of the TCA cycle.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
134 145 ProSitePatterns PS00781 Phosphoenolpyruvate carboxylase active site 1.
134 145 InterPro IPR018129 Phosphoenolpyruvate carboxylase, Lys active site
273 388 FunFam G3DSA:1.20.1440.90:FF:000002 Phosphoenolpyruvate carboxylase
8 883 Pfam PF00311 Phosphoenolpyruvate carboxylase
8 883 InterPro IPR021135 Phosphoenolpyruvate carboxylase
3 883 PANTHER PTHR30523 PHOSPHOENOLPYRUVATE CARBOXYLASE
3 883 InterPro IPR021135 Phosphoenolpyruvate carboxylase
6 883 SUPERFAMILY SSF51621 Phosphoenolpyruvate/pyruvate domain
6 883 InterPro IPR015813 Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
273 388 Gene3D G3DSA:1.20.1440.90 Phosphoenolpyruvate/pyruvate domain
537 549 ProSitePatterns PS00393 Phosphoenolpyruvate carboxylase active site 2.
537 549 InterPro IPR033129 Phosphoenolpyruvate carboxylase, His active site
1 883 Hamap MF_00595 Phosphoenolpyruvate carboxylase [ppc].
1 883 InterPro IPR022805 Phosphoenolpyruvate carboxylase, bacterial/plant-type
709 735 PRINTS PR00150 Phosphoenolpyruvate carboxylase signature
709 735 InterPro IPR021135 Phosphoenolpyruvate carboxylase
577 606 PRINTS PR00150 Phosphoenolpyruvate carboxylase signature
577 606 InterPro IPR021135 Phosphoenolpyruvate carboxylase
245 260 PRINTS PR00150 Phosphoenolpyruvate carboxylase signature
245 260 InterPro IPR021135 Phosphoenolpyruvate carboxylase
386 406 PRINTS PR00150 Phosphoenolpyruvate carboxylase signature
386 406 InterPro IPR021135 Phosphoenolpyruvate carboxylase
186 202 PRINTS PR00150 Phosphoenolpyruvate carboxylase signature
186 202 InterPro IPR021135 Phosphoenolpyruvate carboxylase
535 555 PRINTS PR00150 Phosphoenolpyruvate carboxylase signature
535 555 InterPro IPR021135 Phosphoenolpyruvate carboxylase
133 146 PRINTS PR00150 Phosphoenolpyruvate carboxylase signature
133 146 InterPro IPR021135 Phosphoenolpyruvate carboxylase

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 · FPocket

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

Site 1 FPocket #1
0.957
Likely same site as P2Rank 2 3.6 Å 22 shared residues 73% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #2
0.956
Likely same site as P2Rank 3 3.2 Å 23 shared residues 88% of smaller site
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.88
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.846
Likely same site as FPocket 1 3.6 Å 22 shared residues 73% of smaller site
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.744
Likely same site as FPocket 2 3.2 Å 23 shared residues 88% of smaller site
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.56
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.255
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Surrounding area
Residue sets
UniProt: Active site:138-138
UniProt: Active site:546-546
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_A0A0H3GK93
AlphaFold DB full sequence Viewing
ColabFold VK055_3231
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
DCO PDB via homolog 235.0 Da · LogP 0.94 · TPSA 94.8 Open detail RCSB PDB
FLC PDB via homolog Detail RCSB PDB
MLT PDB via homolog Detail RCSB PDB
PG0 PDB via homolog Detail RCSB PDB
ZINC1580161 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
DCO RCSB PDB P00864 235.0 Da LogP 0.94 TPSA 94.8 ✓ Ro5 ✓ Clean C(C(=C(Cl)Cl)C(=O)O)P(=O)(O)O
FLC RCSB PDB P04711 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
MLT RCSB PDB P04711 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)C(=O)O
PG0 RCSB PDB P04711 120.1 Da LogP -0.36 TPSA 38.7 ✓ Ro5 ✓ Clean COCCOCCO

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.