KpATCC43816 Protein target profile

3-octaprenyl-4-hydroxybenzoate decarboxylase together with UbiG

Accession: VK055_4167

Gene: AIK82713.1 ubiX 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A1W1JBQ3

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Length 192

Pocket druggability (P2Rank · AlphaFold DB model) 0.044

Direct ligand evidence 0 33 total records

Functional annotation 1 EC 3 GO

Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 8 structural and 0 bioactivity records.

Risks to review

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: No hit
Gut microbiome similarity: 2.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 58.152 Higher values support similarity to known essential genes.
DEG E-value: 2.22e-71 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 94.98 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) 0.044

Structure A0A1W1JBQ3

Pocket Pocket 1

Druggability (FPocket) 0.47

Structure A0A1W1JBQ3

Pocket Pocket 1

ColabFold model

P2Rank 0.063 · Pocket 1

FPocket 0.408 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 138 / 4744 genomes with a hit

Prevalence 2.9%

Metabolic context

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

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MTPRIIIGISGASGFQYGVKALELLRPLAIEVHLVVSKGAEKTCELETDYRLDEVMALADVVHPINHLGASISSGSFKTLGMLVAPCSMRSLGAIAHCLTDNLLTRAADVVLKERRRLVLLARETPLNLGHIRNMAAVTEMGGIIFPPVPALYQRPQSADDIITHSVNRALDLFDLEVNNIPRWGEGELLYT

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Subcellular localization

Localization: Cytoplasmic

Enzyme Commission (EC)

2.5.1.129

Gene Ontology (GO)

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:0016831 Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
GO:0106141 Catalysis of the reaction: dimethylallyl phosphate + FMNH2 = phosphate + prenyl-FMNH2.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

13 records

Show feature table

Start	End	DB	Term	Name
4	190	Gene3D	G3DSA:3.40.50.1950	-
4	190	InterPro	IPR036551	Flavin prenyltransferase-like
4	184	NCBIfam	TIGR00421	UbiX family flavin prenyltransferase
4	184	InterPro	IPR004507	Flavin prenyltransferase UbiX-like
4	165	Pfam	PF02441	Flavoprotein
4	165	InterPro	IPR003382	Flavoprotein
4	186	SUPERFAMILY	SSF52507	Homo-oligomeric flavin-containing Cys decarboxylases, HFCD
4	186	InterPro	IPR036551	Flavin prenyltransferase-like
3	187	FunFam	G3DSA:3.40.50.1950:FF:000001	Flavin prenyltransferase UbiX
3	186	Hamap	MF_01984	Flavin prenyltransferase UbiX [ubiX].
3	186	InterPro	IPR004507	Flavin prenyltransferase UbiX-like
67	158	PANTHER	PTHR43374	FLAVIN PRENYLTRANSFERASE
67	158	InterPro	IPR004507	Flavin prenyltransferase UbiX-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

0.044

Likely same site as FPocket 1 2.2 Å 8 shared residues 100% of smaller site

Show in viewer

Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1

0.47 Unusual size

Likely same site as P2Rank 1 2.2 Å 8 shared residues 100% of smaller site

Show in viewer

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_A0A1W1JBQ3	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_4167	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.

33 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 8 records from similar proteins

Structural ligands 8 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 25 similarity-based ZINC candidates

Best available ligand signal

4LR PDB via homolog 166.1 Da · LogP 1.06 · TPSA 66.8 Open detail RCSB PDB

4LS PDB via homolog Detail RCSB PDB

4LU PDB via homolog Detail RCSB PDB

DMA PDB via homolog Detail RCSB PDB

FNR PDB via homolog Detail RCSB PDB

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
4LR RCSB PDB	6QLI	A0A072ZCW8	166.1 Da LogP 1.06 TPSA 66.8	✓ Ro5	✓ Clean	`CC(=CCOP(=O)(O)O)C`
4LS RCSB PDB	6QLJ	A0A072ZCW8	526.5 Da LogP 0.43 TPSA 199.6	2 viol.	✓ Clean	`Cc1cc2c(cc1C)N(C3=C(N2CC=C(C)C)C(=O)NC(=O)N3)C[…`
4LU RCSB PDB	6QLK	A0A072ZCW8	525.5 Da LogP -0.09 TPSA 199.4	2 viol.	✓ Clean	`Cc1cc2c3c(c1C)C(CC=[N+]3C4=C(N2C[C@@H]([C@@H]([…`
DMA RCSB PDB	6QLG	A3F715	246.1 Da LogP 1.18 TPSA 113.3	✓ Ro5	✓ Clean	`CC(=CCO[P@@](=O)(O)OP(=O)(O)O)C`
FNR RCSB PDB	6QLH	A0A072ZCW8	458.4 Da LogP -0.93 TPSA 208.4	1 viol.	✓ Clean	`Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C…`
HJN RCSB PDB	6QLV	A0A072ZCW8	594.6 Da LogP 2.15 TPSA 199.6	2 viol.	✓ Clean	`Cc1cc2c(cc1C)N(C3=C(N2C/C=C(/C)\CCC=C(C)C)C(=O)…`
HZZ RCSB PDB	6QLV	A0A072ZCW8	234.2 Da LogP 2.79 TPSA 66.8	✓ Ro5	✓ Clean	`CC(=CCC/C(=C\COP(=O)(O)O)/C)C`
IP8 RCSB PDB	6QLH	A0A072ZCW8	166.1 Da LogP 1.06 TPSA 66.8	✓ Ro5	✓ Clean	`CC(=C)CCOP(=O)(O)O`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC1532829 ZINC	1.000	234.2 Da LogP 2.79 TPSA 66.8	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/COP(=O)(O)O`
ZINC8215740 ZINC	0.692	246.1 Da LogP 1.18 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCO[P@@](=O)(O)OP(=O)(O)O`
ZINC2556391 ZINC	0.655	302.4 Da LogP 4.51 TPSA 66.8	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O)O`
ZINC71769106 ZINC	0.643	326.1 Da LogP 1.30 TPSA 159.8	✓ Ro5	✓ Clean	`CC(C)=CCO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O`
ZINC1677808 ZINC	0.528	210.3 Da LogP 3.63 TPSA 26.3	✓ Ro5	✓ Clean	`CCC(=O)OC/C=C(\C)CCC=C(C)C`
ZINC1850861 ZINC	0.528	224.3 Da LogP 3.88 TPSA 26.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/COC(=O)C(C)C`
ZINC1850863 ZINC	0.528	224.3 Da LogP 3.88 TPSA 26.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C\COC(=O)C(C)C`
ZINC1851030 ZINC	0.528	210.3 Da LogP 3.63 TPSA 26.3	✓ Ro5	✓ Clean	`CCC(=O)OC/C=C(/C)CCC=C(C)C`
ZINC2038091181 ZINC	0.528	224.3 Da LogP 3.88 TPSA 26.3	✓ Ro5	✓ Clean	`CC(C)=CCCC(C)=CCOC(=O)C(C)C`
ZINC1677814 ZINC	0.514	224.3 Da LogP 4.02 TPSA 26.3	✓ Ro5	✓ Clean	`CCCC(=O)OC/C=C(\C)CCC=C(C)C`
ZINC1716708 ZINC	0.514	238.3 Da LogP 3.20 TPSA 43.4	✓ Ro5	✓ Clean	`CC(=O)CC(=O)OC/C=C(\C)CCC=C(C)C`
ZINC1850911 ZINC	0.514	224.3 Da LogP 4.02 TPSA 26.3	✓ Ro5	✓ Clean	`CCCC(=O)OC/C=C(/C)CCC=C(C)C`
ZINC2036789 ZINC	0.514	236.4 Da LogP 4.19 TPSA 26.3	✓ Ro5	✓ Clean	`C/C=C(\C)C(=O)OC/C=C(\C)CCC=C(C)C`
ZINC2036790 ZINC	0.514	236.4 Da LogP 4.19 TPSA 26.3	✓ Ro5	✓ Clean	`C/C=C(/C)C(=O)OC/C=C(\C)CCC=C(C)C`
ZINC2036791 ZINC	0.514	236.4 Da LogP 4.19 TPSA 26.3	✓ Ro5	✓ Clean	`C/C=C(\C)C(=O)OC/C=C(/C)CCC=C(C)C`
ZINC2036792 ZINC	0.514	236.4 Da LogP 4.19 TPSA 26.3	✓ Ro5	✓ Clean	`C/C=C(/C)C(=O)OC/C=C(/C)CCC=C(C)C`
ZINC2053466651 ZINC	0.514	224.3 Da LogP 4.02 TPSA 26.3	✓ Ro5	✓ Clean	`CCCC(=O)OCC=C(C)CCC=C(C)C`
ZINC5082886 ZINC	0.514	238.3 Da LogP 3.20 TPSA 43.4	✓ Ro5	✓ Clean	`CC(=O)CC(=O)OC/C=C(/C)CCC=C(C)C`
ZINC1632634 ZINC	0.500	222.3 Da LogP 3.80 TPSA 26.3	✓ Ro5	✓ Clean	`C/C=C/C(=O)OC/C=C(/C)CCC=C(C)C`
ZINC17014702 ZINC	0.500	222.3 Da LogP 3.80 TPSA 26.3	✓ Ro5	✓ Clean	`C/C=C/C(=O)OC/C=C(\C)CCC=C(C)C`
ZINC17378881 ZINC	0.500	222.3 Da LogP 3.80 TPSA 26.3	✓ Ro5	✓ Clean	`C/C=C\C(=O)OC/C=C(/C)CCC=C(C)C`
ZINC2038251 ZINC	0.500	238.4 Da LogP 4.27 TPSA 26.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/COC(=O)CC(C)C`
ZINC2038252 ZINC	0.500	238.4 Da LogP 4.27 TPSA 26.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C\COC(=O)CC(C)C`
ZINC4974305 ZINC	0.500	222.3 Da LogP 3.80 TPSA 26.3	✓ Ro5	✓ Clean	`C/C=C\C(=O)OC/C=C(\C)CCC=C(C)C`
ZINC8215849 ZINC	0.500	314.2 Da LogP 2.91 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CO[P@@](=O)(O)OP(=O)(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.

Sequence

UniProt A0A1W1JBQ3