Protein target profile

VK055_0340

2,3-dihydroxyphenylpropionate/2, 3-dihydroxicinnamic acid 1,2-dioxygenase

Genome: KpATCC43816 Gene: AIK78966.1 mhpB 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A422ZGW4

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Length 314

Pocket druggability 0.962

Metabolic reactions 2

Chokepoint Yes

Direct ligand evidence 0 52 total records

Functional annotation 1 EC 7 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 bottleneck Catalyzes a reaction that is the only producer or consumer of a metabolite in the imported metabolic model. Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.96, P2Rank 0.76). Use the 3D pocket comparison to verify whether they identify the same site. Central metabolic position More central than 91.9% of genes in this genome. No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. 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: 0.6% 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.

Localization

Localization: Unknown

Structure confidence

ColabFold pLDDT: 96.81 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.962

Structure A0A422ZGW4

Pocket Pocket 1

P2Rank 0.759

Structure A0A422ZGW4

Pocket Pocket 1

ColabFold model

FPocket 0.857 · Pocket 1

P2Rank 0.829 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 27 / 4744 genomes with a hit

Prevalence 0.6%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A422ZGW4

Pathways

KEGG R04376 BioCyc 1.13.11.16-RXN KEGG R06788 BioCyc RXN-12073

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a consuming chokepoint reaction in Phenylalanine metabolism, no isoenzyme backup detected, more central than 91.9% of genes in this genome, no human homolog detected.

Relative network centrality 91.9% more central than 91.9% of genes in this genome

Chokepoint Chokepoint gene

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MHAYLHCLSHTPLVGFVDPEQAVLDEVNGVIADARRRIAEFDPELVVLFAPDHYNGFFYDVMPPFCLGVGAAAIGDFASAAGDLPVPAELAEACAHAILNSGIDLAVSYNMQVDHGFAQPLEFLLGGLDRVPVLPVFINGVAAPLPGFQRTRLLGEAMGRFLNTLNKRVLILGSGGLSHQPPVPELAKADAHLRDRLLGGGKQLPPDERELRQQRVISAARRFTEDPHSLHPLNPVWDNRFMSLLEQGRLSELDAIGNDELSAMAGKSTHEIKTWVAAFAALSAFGRWRSEGRYYRPIPEWIAGFGSLSATTEI

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1.13.11.16

Gene Ontology (GO)

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:0047070 Catalysis of the reaction: O2 + 3-(2,3-dihydroxyphenyl)propanoate = 2-hydroxy-6-oxonona-2,4-diene-1,9-dioate.
GO:0005506 Binding to an iron (Fe) ion.
GO:0008198 Binding to a ferrous iron ion, Fe(II).
GO:0019439 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
GO:0019380 The chemical reactions and pathways resulting in the breakdown of 3-phenylpropionate, the anion of phenylpropanoic acid.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

8 records

Show feature table

Start	End	DB	Term	Name
1	313	Hamap	MF_01653	2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase [mhpB].
1	313	InterPro	IPR023789	2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
3	313	Gene3D	G3DSA:3.40.830.10	-
1	311	CDD	cd07365	MhpB_like
1	311	InterPro	IPR023789	2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
4	306	Pfam	PF02900	Catalytic LigB subunit of aromatic ring-opening dioxygenase
4	306	InterPro	IPR004183	Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B
5	309	SUPERFAMILY	SSF53213	LigB-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 · FPocket

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

Site 1 FPocket #1

0.962

Likely same site as P2Rank 1 1.2 Å 16 shared residues 100% of smaller site

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Surrounding area

Site 2 FPocket #3

0.465

Likely same site as P2Rank 2 1.8 Å 12 shared residues 92% of smaller site

Unusual size

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Surrounding area

Site 3 FPocket #2

0.265

Unusual size

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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1

0.759

Likely same site as FPocket 1 1.2 Å 16 shared residues 100% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.216

Likely same site as FPocket 3 1.8 Å 12 shared residues 92% of smaller site

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Surrounding area

Site 3 P2Rank #3

0.086

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Surrounding area

Site 4 P2Rank #4

0.072

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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1

0.829

Likely same site as FPocket 1 5.8 Å 14 shared residues 70% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.21

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Surrounding area

Site 3 P2Rank #3

0.104

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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_A0A422ZGW4	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_0340	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

DHB PDB via homolog 154.1 Da · LogP 0.80 · TPSA 77.8 Open detail RCSB PDB

GDE PDB via homolog Detail RCSB PDB

ZINC148781474 ZINC proposed compound · Tanimoto 0.727 Detail ZINC

ZINC1675321 ZINC proposed compound · Tanimoto 0.714 Detail ZINC

ZINC12471554 ZINC proposed compound · Tanimoto 0.640 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
DHB RCSB PDB	1B4U	P22636	154.1 Da LogP 0.80 TPSA 77.8	✓ Ro5	Alert	`c1cc(c(cc1C(=O)O)O)O`
GDE RCSB PDB	3WR9	Q5NTE5	170.1 Da LogP 0.50 TPSA 98.0	✓ Ro5	Alert	`c1c(cc(c(c1O)O)O)C(=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
ZINC148781474 ZINC	0.727	274.2 Da LogP 2.16 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)cc2O)c(O)c1`
ZINC1675321 ZINC	0.714	274.2 Da LogP 1.57 TPSA 115.1	✓ Ro5	Alert	`O=C(C(=O)c1ccc(O)c(O)c1)c1ccc(O)c(O)c1`
ZINC12471554 ZINC	0.640	217.0 Da LogP 1.85 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Br)c(O)c1`
ZINC161925 ZINC	0.640	264.0 Da LogP 1.69 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(I)c(O)c1`
ZINC2566180 ZINC	0.640	217.0 Da LogP 1.85 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(O)c(Br)c1`
ZINC330968 ZINC	0.640	264.0 Da LogP 1.69 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(O)c(I)c1`
ZINC6535079 ZINC	0.640	204.2 Da LogP 1.95 TPSA 77.8	✓ Ro5	Alert	`O=C(O)c1ccc2cc(O)c(O)cc2c1`
ZINC262158 ZINC	0.615	214.2 Da LogP 2.33 TPSA 57.5	✓ Ro5	Alert	`O=C(c1ccccc1)c1ccc(O)c(O)c1`
ZINC65350651 ZINC	0.615	258.2 Da LogP 2.46 TPSA 94.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)cc2O)cc1`
ZINC2572877 ZINC	0.593	206.1 Da LogP 2.11 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(O)c(C(F)(F)F)c1`
ZINC44559904 ZINC	0.593	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccccc2)c(O)c1`
ZINC71260675 ZINC	0.593	206.1 Da LogP 2.11 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(F)(F)F)c(O)c1`
ZINC142873985 ZINC	0.586	222.1 Da LogP 1.99 TPSA 66.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(O)c(OC(F)(F)F)c1`
ZINC21950888 ZINC	0.571	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(O)c(-c2ccccc2)c1`
ZINC21967846 ZINC	0.571	217.2 Da LogP -0.26 TPSA 117.7	✓ Ro5	✓ Clean	`NS(=O)(=O)c1cc(C(=O)O)ccc1O`
ZINC65350194 ZINC	0.571	248.2 Da LogP 2.60 TPSA 77.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(F)cc2O)c(O)c1`
ZINC156288 ZINC	0.565	216.2 Da LogP 2.24 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc2cc(C(=O)O)ccc2c1`
ZINC3983883 ZINC	0.556	262.2 Da LogP 1.45 TPSA 118.2	✓ Ro5	Alert	`O=C(c1ccc(O)c(O)c1)c1c(O)cc(O)cc1O`
ZINC2048532784 ZINC	0.542	248.2 Da LogP 1.65 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)c1cc(O)c2cc(C(=O)O)cc(O)c2c1`
ZINC2528279 ZINC	0.542	216.2 Da LogP 2.24 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc2ccc(C(=O)O)cc2c1`
ZINC2579274 ZINC	0.542	240.2 Da LogP 2.73 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc2c(c1)-c1ccc(C(=O)O)cc1-2`
ZINC642881183 ZINC	0.538	350.3 Da LogP 3.83 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2cc(O)c(-c3ccc(C(=O)O)cc3)cc2O)cc1`
ZINC202705328 ZINC	0.536	334.3 Da LogP 1.52 TPSA 133.5	✓ Ro5	Alert	`O=C(OCCOC(=O)c1ccc(O)c(O)c1)c1ccc(O)c(O)c1`
ZINC22005628 ZINC	0.536	248.7 Da LogP 2.98 TPSA 57.5	✓ Ro5	Alert	`O=C(c1ccc(Cl)cc1)c1ccc(O)c(O)c1`
ZINC77286769 ZINC	0.536	228.2 Da LogP 2.64 TPSA 57.5	✓ Ro5	Alert	`Cc1ccc(C(=O)c2ccc(O)c(O)c2)cc1`
ZINC142447986 ZINC	0.533	211.2 Da LogP -0.09 TPSA 106.9	✓ Ro5	Alert	`O=C(O)CNC(=O)c1ccc(O)c(O)c1`
ZINC5664846 ZINC	0.533	284.2 Da LogP 1.57 TPSA 111.9	✓ Ro5	Alert	`O=C(O)c1ccc2c(c1)C(=O)c1c(O)ccc(O)c1C2=O`
ZINC685964134 ZINC	0.533	243.1 Da LogP 2.46 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(O)c(/C=C/Br)c1`
ZINC96027101 ZINC	0.533	223.3 Da LogP 1.62 TPSA 60.8	✓ Ro5	Alert	`CN(C)C(C)(C)C(=O)c1ccc(O)c(O)c1`
ZINC105301 ZINC	0.520	210.1 Da LogP 0.78 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)O)c(C(=O)O)c1`
ZINC2599161 ZINC	0.520	266.3 Da LogP 3.39 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc2cc3cc(C(=O)O)ccc3cc2c1`
ZINC5046520 ZINC	0.520	280.0 Da LogP 1.40 TPSA 77.8	✓ Ro5	✓ Clean	`O=C(O)c1cc(O)c(I)c(O)c1`
ZINC56611 ZINC	0.520	233.0 Da LogP 1.56 TPSA 77.8	✓ Ro5	✓ Clean	`O=C(O)c1cc(O)c(Br)c(O)c1`
ZINC1701223 ZINC	0.519	302.2 Da LogP 1.73 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(c1ccc(O)c(C(=O)O)c1)c1ccc(O)c(C(=O)O)c1`
ZINC211753720 ZINC	0.519	235.0 Da LogP 1.99 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cc(F)c(O)c(Br)c1`
ZINC13334596 ZINC	0.516	222.2 Da LogP 2.30 TPSA 77.8	✓ Ro5	Alert	`CC(C)=CCc1cc(C(=O)O)cc(O)c1O`
ZINC1602813 ZINC	0.516	223.3 Da LogP 1.62 TPSA 60.8	✓ Ro5	Alert	`CCN(CC)CC(=O)c1ccc(O)c(O)c1`
ZINC214590290 ZINC	0.516	205.2 Da LogP 0.67 TPSA 88.2	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-n2cnnc2)c(O)c1`
ZINC214590587 ZINC	0.516	205.2 Da LogP 0.67 TPSA 88.2	✓ Ro5	✓ Clean	`O=C(O)c1ccc(O)c(-n2cnnc2)c1`
ZINC266927 ZINC	0.516	231.3 Da LogP 2.50 TPSA 62.5	✓ Ro5	Alert	`Cc1ccc(C)n1-c1cc(C(=O)O)ccc1O`
ZINC266928 ZINC	0.516	231.3 Da LogP 2.50 TPSA 62.5	✓ Ro5	Alert	`Cc1ccc(C)n1-c1ccc(C(=O)O)cc1O`
ZINC9553364 ZINC	0.516	488.4 Da LogP 0.70 TPSA 193.2	✓ Ro5	✓ Clean	`O=C(O)c1ccc(O)c(-n2c(=O)c3cc4c(=O)n(-c5cc(C(=O)…`
ZINC95933655 ZINC	0.516	204.1 Da LogP 1.69 TPSA 66.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(OC(F)F)c(O)c1`
ZINC96527995 ZINC	0.516	202.2 Da LogP 2.55 TPSA 57.5	✓ Ro5	✓ Clean	`Cc1c(O)ccc2cc(C(=O)O)ccc12`
ZINC96027162 ZINC	0.515	263.3 Da LogP 2.55 TPSA 60.8	✓ Ro5	Alert	`CC(C)(C(=O)c1ccc(O)c(O)c1)N1CCCCC1`
ZINC114059319 ZINC	0.500	202.1 Da LogP 1.36 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1cc(F)c(C(=O)O)c(F)c1`
ZINC1685914 ZINC	0.500	230.2 Da LogP 1.27 TPSA 61.4	✓ Ro5	Alert	`O=C(C[n+]1ccccc1)c1ccc(O)c(O)c1`
ZINC222780355 ZINC	0.500	228.2 Da LogP 0.04 TPSA 124.3	✓ Ro5	Alert	`O=C(O)COC(=O)c1cc(O)c(O)c(O)c1`
ZINC37473956 ZINC	0.500	211.2 Da LogP 1.27 TPSA 95.9	✓ Ro5	✓ Clean	`COC(=O)Nc1ccc(C(=O)O)cc1O`
ZINC57340245 ZINC	0.500	231.2 Da LogP -0.00 TPSA 103.7	✓ Ro5	✓ Clean	`CNS(=O)(=O)c1cc(C(=O)O)ccc1O`

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.