KpATCC43816 Protein target profile

3-octaprenyl-4-hydroxybenzoate decarboxylase

Accession: VK055_3138

Gene: AIK81710.1 ubiD 3D evidence: AlphaFold DB model + ColabFold model Metabolism 4 reactions UniProt A0A0H3GKH2
Length 491
Pocket druggability (P2Rank · AlphaFold DB model) 0.869
Metabolic reactions 4
Chokepoint No
Direct ligand evidence 0 72 total records
Functional annotation 1 EC 6 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
3.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
93.59 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) 0.869
Structure A0A0H3GKH2
Pocket Pocket 1
Druggability (FPocket) 0.578
Structure A0A0H3GKH2
Pocket Pocket 17
ColabFold model
P2Rank 0.84 · Pocket 1
FPocket 0.371 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 157 / 4744 genomes with a hit
Prevalence 3.3%

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 90.7% of genes in this genome, no human homolog detected.

Relative network centrality 90.7% more central than 90.7% 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

4 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.

MKYHDLRDFLTLLEQQGELKRITLPVDPHLEITEIADRTLRAGGPALLFENPKGYTMPVLCNLFGTPRRVALGMGQEDVSSLREVGKLLAFLKEPEPPKGFRDLFDKLPQFKQVLNMPTKRLRGAPCQQKIIQGDDVDLNKIPIMTCWPEDAAPLITWGLTVTRGPHKERQNLGIYRQQLIGKNKLIMRWLSHRGGALDFQEWCAARPGERFPVSVALGADPATILGAVTPVPDTLSEYAFAGLLRGTKTEVVKCVSNDLEVPASAEIVLEGYIEAGEMAPEGPYGDHTGYYNEVDQFPVFTVTHITQREDAIYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPEIVDFYLPPEGCSYRLAVVTMKKQYAGHAKRVMMGVWSFLRQFMYTKFVIVCDDDVNARDWNDVIWAITTRMDPARDTVLVENTPIDYLDFASPVSGLGSKMGLDATNKWPGETQREWGRPIKKDPAVTARIDAIWDELAIFKQQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0008694 Catalysis of the reaction: a 4-hydroxy-3-(all-trans-polyprenyl)benzoate + H+ = a 2-(all-trans-polyprenyl)phenol + CO2.
  • GO:0016831 Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
  • GO:0006744 The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.
  • 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
337 454 FunFam G3DSA:3.40.1670.10:FF:000001 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
1 485 PANTHER PTHR30108 3-OCTAPRENYL-4-HYDROXYBENZOATE CARBOXY-LYASE-RELATED
1 485 InterPro IPR002830 UbiD decarboxylyase family
337 454 Gene3D G3DSA:3.40.1670.10 -
1 487 Hamap MF_01636 3-octaprenyl-4-hydroxybenzoate carboxy-lyase [ubiD].
1 487 InterPro IPR023677 UbiD decarboxylyase, bacteria
11 431 Pfam PF01977 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
11 431 InterPro IPR002830 UbiD decarboxylyase family
3 322 SUPERFAMILY SSF50475 FMN-binding split barrel
455 491 Gene3D G3DSA:1.20.5.570 Single helix bin
455 491 FunFam G3DSA:1.20.5.570:FF:000001 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
323 486 SUPERFAMILY SSF143968 UbiD C-terminal domain-like
6 455 NCBIfam TIGR00148 UbiD family decarboxylase
6 455 InterPro IPR002830 UbiD decarboxylyase family

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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
0.869
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.303
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.053
Likely same site as FPocket 7 5.4 Å 9 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.039
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.029
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #17
0.578
Show in viewer
Surrounding area
Pocket 2 FPocket #7
0.343
Likely same site as P2Rank 3 5.4 Å 9 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 3 FPocket #6
0.211
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:287-287 Proton donor
UniProt: Binding site:172-172
UniProt: Binding site:175-177
UniProt: Binding site:189-191
UniProt: Binding site:194-195
UniProt: Binding site:238-238
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_A0A0H3GKH2
AlphaFold DB full sequence Viewing
ColabFold VK055_3138
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.

72 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 22 records from similar proteins
Structural ligands 22 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
4LU PDB via homolog 525.5 Da · LogP -0.09 · TPSA 199.4 Open detail RCSB PDB
4LV PDB via homolog Detail RCSB PDB
4LW PDB via homolog Detail RCSB PDB
4M4 PDB via homolog Detail RCSB PDB
4MJ 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
4LU RCSB PDB P0AAB4 525.5 Da LogP -0.09 TPSA 199.4 2 viol. ✓ Clean Cc1cc2c3c(c1C)C(CC=[N+]3C4=C(N2C[C@@H]([C@@H]([…
4LV RCSB PDB A2QHE5 162.2 Da LogP 2.17 TPSA 37.3 ✓ Ro5 ✓ Clean C/C(=C\c1ccccc1)/C(=O)O
4LW RCSB PDB A2QHE5 166.2 Da LogP 2.08 TPSA 37.3 ✓ Ro5 ✓ Clean c1ccc(cc1)/C=C(/C(=O)O)\F
4M4 RCSB PDB A2QHE5 150.2 Da LogP 2.04 TPSA 29.5 ✓ Ro5 ✓ Clean COc1cc(ccc1O)C=C
4MJ RCSB PDB A2QHE5 644.6 Da LogP 1.32 TPSA 216.7 2 viol. ✓ Clean Cc1cc2c3c(c1C)C(C[C@H](N3C4=C(N2C[C@@H]([C@@H](…
4VP RCSB PDB Q03034 120.2 Da LogP 2.04 TPSA 20.2 ✓ Ro5 ✓ Clean C=Cc1ccc(cc1)O
7D9 RCSB PDB P0AAB5 606.5 Da LogP -0.64 TPSA 254.0 3 viol. ✓ Clean Cc1cc2c3c(c1C)C(C[C@H](N3C4=C(N2C[C@@H]([C@@H](…
BYN RCSB PDB A2QHE5 542.5 Da LogP -0.13 TPSA 220.1 3 viol. ✓ Clean Cc1cc2c3c(c1C)C(C[C@H](N3C4=C(N2C[C@@H]([C@@H](…
CO2 RCSB PDB A2QHE5 44.0 Da LogP -0.58 TPSA 34.1 ✓ Ro5 ✓ Clean C(=O)=O
F5C RCSB PDB A2QHE5 238.1 Da LogP 2.48 TPSA 37.3 ✓ Ro5 ✓ Clean C(=C/C(=O)O)\c1c(c(c(c(c1F)F)F)F)F
FZZ RCSB PDB A2QHE5 524.5 Da LogP 0.54 TPSA 209.0 2 viol. ✓ Clean Cc1cc2c3c(c1C)C(CC3=NC4=C(N2C[C@@H]([C@@H]([C@@…
JQ8 RCSB PDB A2QHE5 146.1 Da LogP 1.12 TPSA 37.3 ✓ Ro5 ✓ Clean c1ccc(cc1)C#CC(=O)O
JQH RCSB PDB A2QHE5 626.6 Da LogP 1.66 TPSA 192.5 2 viol. ✓ Clean Cc1cc2c3c(c1C)C(C[C@@H]4[N@]3[C@]5(C(=C4)c6cccc…
JQK RCSB PDB A2QHE5 630.6 Da LogP 2.56 TPSA 199.9 2 viol. ✓ Clean Cc1cc2c3c(c1C)C(C[C@H](N3C4=C(N2C[C@@H]([C@@H](…
JQQ RCSB PDB A2QHE5 648.6 Da LogP 2.50 TPSA 199.9 2 viol. ✓ Clean Cc1cc2c3c(c1C)C(C[C@H](N3C4=C(N2C[C@@H]([C@@H](…
JQZ RCSB PDB A2QHE5 CC1=CC2=[N](C3=C4(C(=C([C@H]5[N]4=C2C(=C1C)C(C5…
JRH RCSB PDB A2QHE5 566.5 Da LogP 0.60 TPSA 192.5 2 viol. ✓ Clean Cc1cc2c3c(c1C)C(C[C@@H]4[N@]3[C@]5([C@@H](C4)C)…
JRK RCSB PDB A2QHE5 608.5 Da LogP -0.03 TPSA 229.8 2 viol. ✓ Clean Cc1cc2c3c(c1C)C(C[C@@H]4[N@]3[C@]5(C(=C4C(=O)O)…
JRN RCSB PDB A2QHE5 720.6 Da LogP 1.30 TPSA 200.9 2 viol. ✓ Clean Cc1cc2c3c(c1C)C(C[C@H]([n+]3c4c([n+]2C[C@@H]([C…
JSH RCSB PDB A2QHE5 628.6 Da LogP 1.75 TPSA 192.5 2 viol. ✓ Clean Cc1cc2c3c(c1C)C(C[C@@H]4[N@]3[C@]5([C@@H](C4)c6…
SYN RCSB PDB A2QHE5 104.2 Da LogP 2.33 TPSA 0.0 ✓ Ro5 ✓ Clean C=Cc1ccccc1
TCA RCSB PDB A2QHE5 148.2 Da LogP 1.78 TPSA 37.3 ✓ Ro5 ✓ Clean c1ccc(cc1)\C=C\C(=O)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.