KpATCC43816 Protein target profile

undecaprenyl-diphosphatase UppP

Accession: VK055_4011

Gene: AIK82558.1 uppP 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GVS2
Length 273
Pocket druggability (P2Rank · AlphaFold DB model) 0.882
Metabolic reactions 2
Chokepoint No
Direct ligand evidence 0 52 total records
Functional annotation 1 EC 8 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
3.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
45.936 Higher values support similarity to known essential genes.
DEG E-value
6.59e-72 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
95.65 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) 0.882
Structure A0A0H3GVS2
Pocket Pocket 1
Druggability (FPocket) 0.843
Structure A0A0H3GVS2
Pocket Pocket 7
ColabFold model
P2Rank 0.812 · Pocket 1
FPocket 0.882 · Pocket 11
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 146 / 4744 genomes with a hit
Prevalence 3.1%

Metabolic context

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

Explore metabolic network

Metabolic context: no human homolog detected.

Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

Catalyzed reactions

2 reactions 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.

MSDIHSLLVAAILGVVEGLTEFLPVSSTGHMIIVGHLLGFEGDTANTFEVVIQLGSILAVVVMFWRRLFGLIGIHFGKPPAHEGQGSGRLSLIHILLGMIPAVVMGLIFHDTIKSLFNPVNVMYALVVGGVLLIAAEVLKPKQPRAVGIDDMTYRQAFVIGCFQCLALWPGFSRSGATISGGMLMGVSRYAASEFSFLLAVPMMMGATVLDVYKSIGFLNMGDVPMFAVGFVMAFIVALIAIKTFLQLIKRISFIPFAIYRFIVAAAVYVVFF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Subcellular localization

Localization
CytoplasmicMembrane

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0016311 The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
  • GO:0050380 Catalysis of the reaction: di-trans,octa-cis-undecaprenyl diphosphate + H2O = di-trans,octa-cis-undecaprenyl phosphate + H+ + phosphate.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
  • GO:0009252 The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.
  • GO:0008360 Any process that modulates the surface configuration of a cell.
  • GO:0046677 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

35 records
Show feature table
Start End DB Term Name
273 273 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 18 Phobius SIGNAL_PEPTIDE Signal peptide region
247 251 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
173 191 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
13 35 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
224 246 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 18 SignalP_EUK SignalP-TM SignalP-TM
90 110 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
214 224 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
6 13 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
111 121 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
90 112 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
122 139 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
10 265 NCBIfam TIGR00753 undecaprenyl-diphosphatase UppP
10 265 InterPro IPR003824 Undecaprenyl-diphosphatase UppP
14 18 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
252 272 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
225 246 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
50 69 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
141 151 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
5 272 Hamap MF_01006 Undecaprenyl-diphosphatase [uppP].
5 272 InterPro IPR003824 Undecaprenyl-diphosphatase UppP
122 140 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
70 89 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
19 49 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
187 209 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
192 213 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
253 272 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
50 69 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
152 172 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
6 272 PANTHER PTHR30622 UNDECAPRENYL-DIPHOSPHATASE
6 272 InterPro IPR003824 Undecaprenyl-diphosphatase UppP
10 266 Pfam PF02673 Bacitracin resistance protein BacA
10 266 InterPro IPR003824 Undecaprenyl-diphosphatase UppP

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
0.882
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Surrounding area
Pocket 2 P2Rank #2
0.074
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Surrounding area
Pocket 3 P2Rank #3
0.049
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Surrounding area
Pocket 4 P2Rank #4
0.033
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Surrounding area
Pocket 5 P2Rank #5
0.017
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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 #7
0.843
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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_A0A0H3GVS2
AlphaFold DB full sequence Viewing
ColabFold VK055_4011
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
FLC PDB via homolog 189.1 Da · LogP -5.25 · TPSA 140.6 Open detail RCSB PDB
OLC PDB via homolog Detail RCSB PDB
ZINC1501016272 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC1501016273 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC1501016315 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
FLC RCSB PDB P60932 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
OLC RCSB PDB P60932 356.5 Da LogP 4.92 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H](CO)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.