KpATCC43816 Protein target profile

phenolic acid decarboxylase subunit C

Accession: VK055_4419

Gene: AIK82962.1 bsdC 3D evidence: AlphaFold DB model + ColabFold model Metabolism 4 reactions UniProt A0A0H3GS97

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Length 475

Pocket druggability (P2Rank · AlphaFold DB model) 0.923

Metabolic reactions 4

Chokepoint Yes

Direct ligand evidence 0 40 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.

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 96.1% of genes in this genome. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Review the complete evidence below

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: 1.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 31.084 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT: 95.56 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) 0.923

Structure A0A0H3GS97

Pocket Pocket 1

Druggability (FPocket) 0.778

Structure A0A0H3GS97

Pocket Pocket 19

ColabFold model

P2Rank 0.948 · Pocket 1

FPocket 0.803 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 79 / 4744 genomes with a hit

Prevalence 1.7%

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a producing chokepoint reaction in Aminobenzoate degradation, more central than 96.1% of genes in this genome, no human homolog detected.

Relative network centrality 96.1% more central than 96.1% of genes in this genome

Chokepoint Chokepoint gene

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MAFDDLRSFLQALDDQGQLLKISEEVNAEPDLAAAANATGRIGDGAPALWFDNIRGFNDARVTMNTIGSWQNHAISLGLPPNTPVKKQIDEFIRRWDNFPVTPERRANPAWAENTVDGDDINLFDILPLFRLNDGDGGFYLDKACVVSRDPLDKDNFGKQNVGIYRMEVKGKRKLGLQPVPMHDIALHLHKAEERGEDLPIAITLGNDPIITLMGATPLKYDQSEYEMAGALRESPYPIATAPLTGFDVPWGSEVILEGVIEGRKREIEGPFGEFTGHYSGGRNMTVVRIDKVSYRSKPIFESLYLGMPWTEIDYLMGPATCVPLYQQLKAEFPEVQAVNAMYTHGLLAIISTKKRYGGFARAVGLRAMTTPHGLGYVKMVIMVDEDVDPFNLPQVMWALSSKVNPAGDLVQLPNMSVLELDPGSSPAGITDKLIIDATTPVAPDLRGHYSQPVQDLPETKAWAEKLTAMLANRK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization: Cytoplasmic

Enzyme Commission (EC)

4.1.1.-

Gene Ontology (GO)

GO:0016831 Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0008694 Catalysis of the reaction: a 4-hydroxy-3-(all-trans-polyprenyl)benzoate + H+ = a 2-(all-trans-polyprenyl)phenol + CO2.
GO:0046872 Binding to a metal ion.
GO:0009636 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 a toxic stimulus.
GO:0006744 The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

13 records

Show feature table

Start	End	DB	Term	Name
326	439	Gene3D	G3DSA:3.40.1670.10	-
1	472	PANTHER	PTHR30108	3-OCTAPRENYL-4-HYDROXYBENZOATE CARBOXY-LYASE-RELATED
1	472	InterPro	IPR002830	UbiD decarboxylyase family
3	309	SUPERFAMILY	SSF50475	FMN-binding split barrel
10	416	Pfam	PF01977	3-octaprenyl-4-hydroxybenzoate carboxy-lyase
10	416	InterPro	IPR002830	UbiD decarboxylyase family
312	467	SUPERFAMILY	SSF143968	UbiD C-terminal domain-like
326	439	FunFam	G3DSA:3.40.1670.10:FF:000003	Phenolic acid decarboxylase
1	472	Hamap	MF_01985	Phenolic acid decarboxylase.
1	472	InterPro	IPR032902	Phenolic acid decarboxylase subunit C
6	441	NCBIfam	TIGR00148	UbiD family decarboxylase
6	441	InterPro	IPR002830	UbiD decarboxylyase family
4	469	NCBIfam	NF041204	non-oxidative hydroxyarylic acid decarboxylases subunit C

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

0.923

Likely same site as FPocket 19 1.3 Å 27 shared residues 96% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.03

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Surrounding area

Pocket 3 P2Rank #3

0.018

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Surrounding area

Pocket 4 P2Rank #4

0.016

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Surrounding area

Pocket 5 P2Rank #5

0.009

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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 #19

0.778 Unusual size

Likely same site as P2Rank 1 1.3 Å 27 shared residues 96% of smaller site

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Surrounding area

Residue sets

UniProt: Active site:274-274 Proton donor

UniProt: Binding site:161-161

UniProt: Binding site:161-166

UniProt: Binding site:182-183

UniProt: Binding site:183-183

UniProt: Binding site:225-225

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1

0.948

Likely same site as FPocket 1 1.3 Å 26 shared residues 90% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.191

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Surrounding area

Pocket 3 P2Rank #3

0.041

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Surrounding area

Pocket 4 P2Rank #4

0.028

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Surrounding area

Pocket 5 P2Rank #5

0.019

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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 #1

0.803 Unusual size

Likely same site as P2Rank 1 1.3 Å 26 shared residues 90% of smaller site

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Surrounding area

Pocket 2 FPocket #2

0.427

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Surrounding area

Residue sets

UniProt: Active site:274-274 Proton donor

UniProt: Binding site:161-161

UniProt: Binding site:161-166

UniProt: Binding site:182-183

UniProt: Binding site:183-183

UniProt: Binding site:225-225

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_A0A0H3GS97	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_4419	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.

40 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 37 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

7D9 PDB via homolog Detail RCSB PDB

9JE PDB via homolog Detail RCSB PDB

ZINC14771652 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC15269439 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

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
4LU RCSB PDB	6H6X	A5D4Z9	525.5 Da LogP -0.09 TPSA 199.4	2 viol.	✓ Clean	`Cc1cc2c3c(c1C)C(CC=[N+]3C4=C(N2C[C@@H]([C@@H]([…`
7D9 RCSB PDB	5M1E	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](…`
9JE RCSB PDB	5O3M	A6T7M3	104.1 Da LogP 0.14 TPSA 40.5	✓ Ro5	✓ Clean	`C(CCO)CCO`

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
ZINC14771652 ZINC	1.000	216.4 Da LogP 3.26 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCCO`
ZINC15269439 ZINC	1.000	272.5 Da LogP 4.82 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCCCCCCO`
ZINC1574339 ZINC	1.000	202.3 Da LogP 2.87 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCO`
ZINC4202510 ZINC	1.000	230.4 Da LogP 3.65 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCCCO`
ZINC4521552 ZINC	1.000	258.4 Da LogP 4.43 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCCCCCO`
ZINC4600152 ZINC	1.000	244.4 Da LogP 4.04 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCCCCO`
ZINC1644076 ZINC	0.615	214.4 Da LogP 4.68 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCO`
ZINC1680803 ZINC	0.615	200.4 Da LogP 4.29 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCO`
ZINC2385445 ZINC	0.615	201.4 Da LogP 2.84 TPSA 46.2	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCO`
ZINC34196183 ZINC	0.615	229.4 Da LogP 3.62 TPSA 46.2	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCO`
ZINC4501366 ZINC	0.615	204.4 Da LogP 3.42 TPSA 20.2	✓ Ro5	✓ Clean	`OCCCCCCCCCCCS`
ZINC139618309 ZINC	0.571	301.5 Da LogP 4.02 TPSA 52.5	✓ Ro5	✓ Clean	`OCCCCCCCCCNCCCCCCCCCO`
ZINC247757772 ZINC	0.571	254.4 Da LogP 3.66 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCC#CCCCCCCCO`
ZINC261828216 ZINC	0.571	282.5 Da LogP 4.44 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCC#CCCCCCCCCO`
ZINC26897398 ZINC	0.571	206.4 Da LogP 2.04 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCSCCCCCO`
ZINC36468523 ZINC	0.571	256.4 Da LogP 4.21 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCC/C=C\CCCCCCCO`
ZINC62240763 ZINC	0.571	284.5 Da LogP 4.99 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCC/C=C\CCCCCCCCO`
ZINC98090187 ZINC	0.571	217.4 Da LogP 1.68 TPSA 52.5	✓ Ro5	✓ Clean	`OCCCCCCNCCCCCCO`
ZINC113216117 ZINC	0.500	306.4 Da LogP 2.14 TPSA 68.2	✓ Ro5	✓ Clean	`OCCCCOCCCCOCCCCOCCCCO`
ZINC137540565 ZINC	0.500	378.6 Da LogP 2.94 TPSA 77.4	✓ Ro5	✓ Clean	`OCCCCOCCCCOCCCCOCCCCOCCCCO`
ZINC14510370 ZINC	0.500	244.4 Da LogP 3.74 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCO`
ZINC148125630 ZINC	0.500	201.4 Da LogP 2.71 TPSA 32.3	✓ Ro5	✓ Clean	`CNCCCCCCCCCCCO`
ZINC1531061 ZINC	0.500	216.3 Da LogP 2.96 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCO`
ZINC1610426 ZINC	0.500	230.3 Da LogP 3.35 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCO`
ZINC169795588 ZINC	0.500	240.3 Da LogP 4.44 TPSA 20.2	✓ Ro5	✓ Clean	`OCCCCCCCCCCCC(F)(F)F`
ZINC2012426 ZINC	0.500	200.4 Da LogP 4.15 TPSA 20.2	✓ Ro5	✓ Clean	`CC(C)CCCCCCCCCCO`
ZINC2168567 ZINC	0.500	202.3 Da LogP 2.57 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCO`
ZINC33966703 ZINC	0.500	234.3 Da LogP 1.34 TPSA 58.9	✓ Ro5	✓ Clean	`OCCCCOCCCCOCCCCO`
ZINC34564691 ZINC	0.500	238.4 Da LogP 4.68 TPSA 20.2	✓ Ro5	✓ Clean	`C#CCCCCCCCCCCCCCCO`
ZINC34570000 ZINC	0.500	226.4 Da LogP 4.85 TPSA 20.2	✓ Ro5	✓ Clean	`C=CCCCCCCCCCCCCCO`
ZINC34586464 ZINC	0.500	224.4 Da LogP 4.29 TPSA 20.2	✓ Ro5	✓ Clean	`C#CCCCCCCCCCCCCCO`
ZINC3861297 ZINC	0.500	272.4 Da LogP 4.52 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCCO`
ZINC4284502 ZINC	0.500	258.4 Da LogP 4.13 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCO`
ZINC44676392 ZINC	0.500	214.4 Da LogP 4.54 TPSA 20.2	✓ Ro5	✓ Clean	`CC(C)CCCCCCCCCCCO`
ZINC5157674 ZINC	0.500	212.4 Da LogP 4.46 TPSA 20.2	✓ Ro5	✓ Clean	`C=CCCCCCCCCCCCCO`
ZINC5287109 ZINC	0.500	286.5 Da LogP 4.91 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCCCO`
ZINC95884217 ZINC	0.500	210.4 Da LogP 3.90 TPSA 20.2	✓ Ro5	✓ Clean	`C#CCCCCCCCCCCCCO`

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 A0A0H3GS97

Pathways

KEGG R02952 BioCyc RXN-802 BioCyc RXN-21078 KEGG R01238 BioCyc 4-HYDROXYBENZOATE-DECARBOXYLASE-RXN KEGG R11071 BioCyc RXN-801