KpATCC43816 Protein target profile

3,4-dihydroxyphenylacetate 2,3-dioxygenase

Accession: VK055_2653

Gene: AIK81247.1 hpaD 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GHT6

Export view

Length 285

Pocket druggability (P2Rank · AlphaFold DB model) 0.683

Metabolic reactions 1

Chokepoint Yes

Direct ligand evidence 0 53 total records

Functional annotation 0 EC 4 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 94.5% of genes in this genome. No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. 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: 1.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT: 97.0 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) 0.683

Structure A0A0H3GHT6

Pocket Pocket 1

Druggability (FPocket) 0.714

Structure A0A0H3GHT6

Pocket Pocket 9

ColabFold model

P2Rank 0.693 · Pocket 1

FPocket 0.088 · Pocket 14

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 55 / 4744 genomes with a hit

Prevalence 1.2%

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a producing & consuming chokepoint reaction in Tyrosine metabolism, no isoenzyme backup detected, more central than 94.5% of genes in this genome, no human homolog detected.

Relative network centrality 94.5% more central than 94.5% of genes in this genome

Chokepoint Chokepoint gene

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MGKLALAAKITHVPSMYLSELPGKNHGCRQGAIDGHKEIGKRCREMGVDTIIVFDTHWLVNSAYHINCADHFQGVYTSNELPHFIRDMTYDYDGNPELGQLIADEAVKLGVRAKAHNIPSLKLEYGTLVPMRYMNSDKHFKVVSISAFCTVHDFADSRRLGEAILKAIEKYDGTVAVLASGSLSHRFIDDQRAEEGMNSYTREFDHQMDERVVKLWREGKFKEFCTMLPEYADYCYGEGNMHDTVMLLGLLGWDKYDGKVEFITELFASSGTGQVNAVFPLPAQA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

GO:0008198 Binding to a ferrous iron ion, Fe(II).
GO:0006725 OBSOLETE. The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
GO:0008687 Catalysis of the reaction: 3,4-dihydroxyphenylacetate + O2 = 5-formyl-2-hydroxyhepta-2,4-dienedioate + H+.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

9 records

Show feature table

Start	End	DB	Term	Name
10	276	PANTHER	PTHR30096	UNCHARACTERIZED
3	281	Gene3D	G3DSA:3.40.830.10	-
12	279	SUPERFAMILY	SSF53213	LigB-like
3	281	CDD	cd07370	HPCD
3	281	InterPro	IPR011984	3,4-dihydroxyphenylacetate 2,3-dioxygenase
7	279	Pfam	PF02900	Catalytic LigB subunit of aromatic ring-opening dioxygenase
7	279	InterPro	IPR004183	Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B
1	281	NCBIfam	TIGR02298	3,4-dihydroxyphenylacetate 2,3-dioxygenase
1	281	InterPro	IPR011984	3,4-dihydroxyphenylacetate 2,3-dioxygenase

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

0.683

Likely same site as FPocket 9 5.5 Å 11 shared residues 65% of smaller site

Show in viewer

Surrounding area

Pocket 2 P2Rank #2

0.203

Show in viewer

Surrounding area

Pocket 3 P2Rank #3

0.022

Show in viewer

Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #9

0.714 Unusual size

Likely same site as P2Rank 1 5.5 Å 11 shared residues 65% of smaller site

Show in viewer

Surrounding area

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.693

Show in viewer

Surrounding area

Pocket 2 P2Rank #2

0.088

Show in viewer

Surrounding area

Pocket 3 P2Rank #3

0.057

Show in viewer

Surrounding area

Pocket 4 P2Rank #4

0.002

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_A0A0H3GHT6	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_2653	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.

53 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 50 similarity-based ZINC candidates

Best available ligand signal

2X7 PDB via homolog 123.1 Da · LogP 0.12 · TPSA 54.1 Open detail RCSB PDB

2XP PDB via homolog Detail RCSB PDB

4NC PDB via homolog Detail RCSB PDB

ZINC36019045 ZINC proposed compound · Tanimoto 0.720 Detail ZINC

ZINC1726237 ZINC proposed compound · Tanimoto 0.667 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
2X7 RCSB PDB	3VSJ	Q6J1Z6	123.1 Da LogP 0.12 TPSA 54.1	✓ Ro5	✓ Clean	`[H]/N=C/1\C=CC=COC1=O`
2XP RCSB PDB	3VSJ	Q6J1Z6	141.1 Da LogP 0.24 TPSA 78.2	✓ Ro5	✓ Clean	`[H]/N=C(/C/C=C\C=O)\C(=O)O`
4NC RCSB PDB	3VSI	Q6J1Z6	155.1 Da LogP 1.01 TPSA 83.6	✓ Ro5	Alert	`c1cc(c(cc1[N+](=O)[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
ZINC36019045 ZINC	0.720	276.2 Da LogP 2.58 TPSA 126.7	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(-c2cc([N+](=O)[O-])ccc2O)…`
ZINC1726237 ZINC	0.667	265.0 Da LogP 1.90 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(I)c1`
ZINC1750322 ZINC	0.667	218.0 Da LogP 2.06 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(Br)c1`
ZINC352067517 ZINC	0.667	205.2 Da LogP 2.16 TPSA 83.6	✓ Ro5	Alert	`O=[N+]([O-])c1ccc2cc(O)c(O)cc2c1`
ZINC60007417 ZINC	0.667	265.0 Da LogP 1.90 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(I)c(O)c1`
ZINC91682324 ZINC	0.667	218.0 Da LogP 2.06 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(Br)c(O)c1`
ZINC31623633 ZINC	0.643	290.2 Da LogP 2.51 TPSA 126.7	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(Cc2cc([N+](=O)[O-])ccc2O)…`
ZINC12359019 ZINC	0.633	259.2 Da LogP 3.42 TPSA 108.3	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/N=N/c2ccc(O)c(O)c2)cc1`
ZINC96068546 ZINC	0.633	259.2 Da LogP 3.42 TPSA 108.3	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(N=Nc2ccc(O)c(O)c2)cc1`
ZINC68675213 ZINC	0.621	234.2 Da LogP 2.36 TPSA 106.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc2c(O)cc([N+](=O)[O-])cc2c1`
ZINC1724272 ZINC	0.600	219.2 Da LogP 0.55 TPSA 117.7	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(S(=O)(=O)O)c1`
ZINC201968930 ZINC	0.600	218.2 Da LogP -0.05 TPSA 123.5	✓ Ro5	✓ Clean	`NS(=O)(=O)c1ccc([N+](=O)[O-])cc1O`
ZINC32914724 ZINC	0.600	207.1 Da LogP 2.32 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(C(F)(F)F)c1`
ZINC84193183 ZINC	0.600	218.2 Da LogP -0.05 TPSA 123.5	✓ Ro5	✓ Clean	`NS(=O)(=O)c1cc([N+](=O)[O-])ccc1O`
ZINC91366454 ZINC	0.600	207.1 Da LogP 2.32 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(C(F)(F)F)c(O)c1`
ZINC15443205 ZINC	0.581	217.2 Da LogP 0.70 TPSA 97.5	✓ Ro5	✓ Clean	`CS(=O)(=O)c1cc([N+](=O)[O-])ccc1O`
ZINC17158509 ZINC	0.581	330.3 Da LogP 2.37 TPSA 151.5	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(O)c(/C=N\N=C/c2cc([N+](=O)[O-…`
ZINC5732217 ZINC	0.581	330.3 Da LogP 2.37 TPSA 151.5	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(O)c(/C=N\N=C\c2cc([N+](=O)[O-…`
ZINC6861885 ZINC	0.581	330.3 Da LogP 2.37 TPSA 151.5	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(O)c(/C=N/N=C/c2cc([N+](=O)[O-…`
ZINC84191264 ZINC	0.581	215.2 Da LogP 2.97 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(-c2ccccc2)c1`
ZINC95495694 ZINC	0.581	217.2 Da LogP 0.70 TPSA 97.5	✓ Ro5	✓ Clean	`CS(=O)(=O)c1ccc([N+](=O)[O-])cc1O`
ZINC1716715 ZINC	0.563	234.2 Da LogP 2.36 TPSA 106.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc2c([N+](=O)[O-])c(O)ccc2c1`
ZINC4615055 ZINC	0.563	204.2 Da LogP 2.09 TPSA 68.3	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(-n2cccc2)c(O)c1`
ZINC32252508 ZINC	0.560	218.2 Da LogP 2.66 TPSA 86.3	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc2cc([N+](=O)[O-])ccc2c1`
ZINC536953409 ZINC	0.548	249.7 Da LogP 3.62 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(-c2ccc(O)c(Cl)c2)cc1`
ZINC100004378 ZINC	0.545	320.2 Da LogP 2.86 TPSA 161.7	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(Nc2ccc([N+](=O)[O-])cc2[N+](=…`
ZINC146403874 ZINC	0.545	223.1 Da LogP 2.20 TPSA 72.6	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(OC(F)(F)F)c(O)c1`
ZINC2046903 ZINC	0.545	235.2 Da LogP 0.48 TPSA 127.0	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(OS(=O)(=O)O)c1`
ZINC28294429 ZINC	0.545	349.3 Da LogP 1.87 TPSA 150.2	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(O)c(CN(CO)Cc2cc([N+](=O)[O-])…`
ZINC294699 ZINC	0.545	211.2 Da LogP 1.51 TPSA 63.4	✓ Ro5	Alert	`C[N+](C)(C)Cc1ccc([N+](=O)[O-])cc1O`
ZINC35024584 ZINC	0.545	214.3 Da LogP 1.68 TPSA 63.4	✓ Ro5	✓ Clean	`C[S+](C)Cc1cc([N+](=O)[O-])ccc1O`
ZINC4014057 ZINC	0.545	210.2 Da LogP 1.00 TPSA 83.7	✓ Ro5	✓ Clean	`CN(C)C(=O)c1cc([N+](=O)[O-])ccc1O`
ZINC66111171 ZINC	0.545	206.2 Da LogP 0.88 TPSA 94.1	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(-n2cnnc2)c1`
ZINC66111174 ZINC	0.545	206.2 Da LogP 0.88 TPSA 94.1	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(-n2cnnc2)c(O)c1`
ZINC85476722 ZINC	0.545	223.1 Da LogP 2.20 TPSA 72.6	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(OC(F)(F)F)c1`
ZINC5568338 ZINC	0.543	303.2 Da LogP 2.66 TPSA 139.1	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/N=C/c2cc([N+](=O)[O-])ccc2O)…`
ZINC2168662 ZINC	0.538	218.2 Da LogP 2.66 TPSA 86.3	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc2ccc([N+](=O)[O-])cc2c1`
ZINC100456108 ZINC	0.529	287.2 Da LogP 2.96 TPSA 118.9	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/C=N/c2ccc([N+](=O)[O-])cc2O)…`
ZINC103653274 ZINC	0.529	358.3 Da LogP 2.45 TPSA 151.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(/C=N\CC/N=C\c2cc([N+](=O)…`
ZINC15772486 ZINC	0.529	406.4 Da LogP 4.42 TPSA 151.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(/C=N\c2ccc(/N=C/c3cc([N+]…`
ZINC1644610 ZINC	0.529	406.4 Da LogP 4.42 TPSA 151.5	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(O)c(/N=C/c2ccc(/C=N/c3cc([N+]…`
ZINC1670414 ZINC	0.529	358.3 Da LogP 2.45 TPSA 151.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(/C=N/CC/N=C/c2cc([N+](=O)…`
ZINC16997814 ZINC	0.529	406.4 Da LogP 4.42 TPSA 151.5	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(O)c(/N=C\c2ccc(/C=N/c3cc([N+]…`
ZINC20268444 ZINC	0.529	229.2 Da LogP 2.89 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(Cc2ccccc2)c1`
ZINC307639619 ZINC	0.529	265.1 Da LogP 1.60 TPSA 81.8	✓ Ro5	✓ Clean	`CC1(C)OB(c2ccc([N+](=O)[O-])cc2O)OC1(C)C`
ZINC3153934 ZINC	0.529	287.2 Da LogP 2.96 TPSA 118.9	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/C=N/c2cc([N+](=O)[O-])ccc2O)…`
ZINC35583886 ZINC	0.529	243.3 Da LogP 2.78 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(C2SCCS2)c1`
ZINC36020548 ZINC	0.529	438.4 Da LogP 3.42 TPSA 184.9	✓ Ro5	✓ Clean	`O=C(Nc1cc([N+](=O)[O-])ccc1O)c1ccc(C(=O)Nc2cc([…`
ZINC43190938 ZINC	0.529	416.3 Da LogP 1.51 TPSA 167.4	✓ Ro5	✓ Clean	`O=C(c1cc([N+](=O)[O-])ccc1O)N1CCN(C(=O)c2cc([N+…`
ZINC43190941 ZINC	0.529	438.4 Da LogP 3.42 TPSA 184.9	✓ Ro5	✓ Clean	`O=C(Nc1ccc(NC(=O)c2cc([N+](=O)[O-])ccc2O)cc1)c1…`

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 A0A0H3GHT6

Pathways

KEGG R03303 BioCyc 1.13.11.15-RXN