Protein target profile

VK055_0339

3-(3-hydroxy-phenyl)propionate/3-hydroxycinnamic acid hydroxylase

Genome: KpATCC43816 Gene: mhpA AIK78965.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GR47

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Length 554

Pocket druggability 0.986

Metabolic reactions 1

Chokepoint Yes

Direct ligand evidence 0 27 total records

Functional annotation 1 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 bottleneck Catalyzes a reaction that is the only producer or consumer of a metabolite in the imported metabolic model. No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.94. 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: Hit
Human identity (%): 23.214 Lower values reduce human off-target concern.
Human E-value: 6.84e-10
Gut microbiome similarity: 0.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 25.387 Higher values support similarity to known essential genes.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 87.26 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 0.986

Structure A0A0H3GR47

Pocket Pocket 41

P2Rank 0.94

Structure A0A0H3GR47

Pocket Pocket 1

ColabFold model

FPocket 0.917 · Pocket 31

P2Rank 0.987 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 28 / 4744 genomes with a hit

Prevalence 0.6%

Cross-references

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

Sequence

UniProt A0A0H3GR47

Pathways

KEGG R06786 BioCyc MHPHYDROXY-RXN

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 Phenylalanine metabolism, no isoenzyme backup detected.

Relative network centrality 0.0% more central than 0.0% of genes in this genome

Chokepoint Chokepoint gene

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MTTSTPDIQPAVQHTAQVAIVGAGPVGLMMANYLGQMGISVLVVEKLATLIDYPRAIGIDDESLRAMQAVGLVNDVLPHTTPWHAMRFLTPKGRCFADIQPMTDEFGWSRRNAFIQPQVDAVMYHGLQRFPQVRCLFSREVEAFSQTGDSVTLNLKGPDGERETVRADWLVACDGGASFIRRTLNIPFEGKTAPNQWIVIDIANDPLATPHVYLCCDPVRPYVSAALPHGVRRFEFMVMPGETEAQLSEPHNMRRLLSKVLPDPDRVELIRQRVYTHNARLAERFRINRVLLAGDAAHIMPVWQGQGYNSGMRDAFNLAWKLALVVNGKAGEALLDSYQQERRDHAKAMIDLSVTAGYVLAPPKRWQGAVRDGLSWLLNYLPPVKRYFLEMRFKPMPQYREGALLTDGAGKTSPVGKMFIQPQVTLESGESVLLDEVIGANFAIIGWGCNPQWGLDAGQIARWRAIGVRFIQVVPEVQIHREQDNAPGTLRVGDRQNRLKSWFAQHNTAIAVVRPDRFVAALAIPQSLGAQLTALAEKMALATGDTAHAEEKVA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1.14.13.127

Gene Ontology (GO)

GO:0071949 Binding to the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
GO:0019622 The chemical reactions and pathways resulting in the breakdown of 3-(3-hydroxy)phenylpropionate, a hydroxylated derivative of phenylpropionate.
GO:0008688 Catalysis of the reaction: 3-(3-hydroxyphenyl)propionate + NADH + oxygen + H+ = 3-(2,3-dihydroxyphenyl)propionate + NAD+ + H2O.
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.

17 records

Show feature table

Start	End	DB	Term	Name
18	204	FunFam	G3DSA:3.50.50.60:FF:000126	3-(3-hydroxy-phenyl)propionate/3-hydroxycinnamic acid hydroxylase
16	352	Pfam	PF01494	FAD binding domain
16	352	InterPro	IPR002938	FAD-binding domain
7	554	Hamap	MF_01652	3-(3-hydroxy-phenyl)propionate/3-hydroxycinnamic acid hydroxylase [mhpA].
7	554	InterPro	IPR023786	3-(3-hydroxy-phenyl)propionate/3-hydroxycinnamic acid hydroxylase
166	181	PRINTS	PR00420	Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
287	302	PRINTS	PR00420	Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
320	338	PRINTS	PR00420	Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
302	318	PRINTS	PR00420	Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
338	354	PRINTS	PR00420	Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
17	39	PRINTS	PR00420	Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
17	388	SUPERFAMILY	SSF51905	FAD/NAD(P)-binding domain
17	388	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
195	276	Gene3D	G3DSA:3.30.70.2450	-
1	529	PANTHER	PTHR43476	3-(3-HYDROXY-PHENYL)PROPIONATE/3-HYDROXYCINNAMIC ACID HYDROXYLASE
18	351	Gene3D	G3DSA:3.50.50.60	-
18	351	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily

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 #41

0.986

Likely same site as P2Rank 2 2.2 Å 20 shared residues 91% of smaller site

Unusual size

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Surrounding area

Site 2 FPocket #2

0.965

Likely same site as P2Rank 1 1.4 Å 45 shared residues 98% of smaller site

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

0.94

Likely same site as FPocket 2 1.4 Å 45 shared residues 98% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.865

Likely same site as FPocket 41 2.2 Å 20 shared residues 91% of smaller site

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Surrounding area

Site 3 P2Rank #3

0.428

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Surrounding area

Site 4 P2Rank #4

0.174

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Surrounding area

Site 5 P2Rank #5

0.138

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Surrounding area

Residue sets

UniProt: Binding site:17-46

UniProt: Binding site:285-295

Binding pockets · FPocket

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

Site 1 FPocket #31

0.917

Likely same site as P2Rank 2 2.7 Å 16 shared residues 100% of smaller site

Unusual size

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Surrounding area

Site 2 FPocket #39

0.677

Unusual size

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Surrounding area

Site 3 FPocket #4

0.248

Likely same site as P2Rank 1 6.3 Å 41 shared residues 61% of smaller site

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

0.987

Likely same site as FPocket 4 6.3 Å 41 shared residues 61% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.626

Likely same site as FPocket 31 2.7 Å 16 shared residues 100% of smaller site

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Surrounding area

Site 3 P2Rank #3

0.246

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Surrounding area

Site 4 P2Rank #4

0.098

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Surrounding area

Site 5 P2Rank #5

0.082

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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_A0A0H3GR47	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_0339	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.

27 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 5 records from similar proteins

Structural ligands 5 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 22 similarity-based ZINC candidates

Best available ligand signal

PKS PDB via homolog 385.5 Da · LogP 5.45 · TPSA 62.6 Open detail RCSB PDB

PM0 PDB via homolog Detail RCSB PDB

RFH PDB via homolog Detail RCSB PDB

RFP PDB via homolog Detail RCSB PDB

VAK 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
PKS RCSB PDB	6U0S	W0C4C9	385.5 Da LogP 5.45 TPSA 62.6	1 viol.	✓ Clean	`C/C=C(\C)/[C@@H]([C@H](C)/C=C(\C)/C=C/C/C(=C/Cc…`
PM0 RCSB PDB	4K5S	Q194P4	1093.1 Da LogP 0.79 TPSA 355.0	3 viol.	✓ Clean	`Cc1c(cc2cc3c(c(c2c1O)O)C(=O)[C@]4([C@@H](C3)[C@…`
RFH RCSB PDB	6C7S	Q5YTV5	839.0 Da LogP 3.15 TPSA 248.0	2 viol.	Alert	`Cc1c(c2c(c3c1O[C@](C3=O)(C)O/C=C/[C@@H]([C@@H](…`
RFP RCSB PDB	6BRD	F2R776	823.0 Da LogP 4.34 TPSA 220.1	3 viol.	Alert	`Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C…`
VAK RCSB PDB	3IHG	Q54530	412.4 Da LogP 1.71 TPSA 141.4	✓ Ro5	Alert	`CC[C@]1(C[C@@H](c2c(cc3c(c2O)C(=O)c4c(cccc4O)C3…`

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
ZINC4654750 ZINC	1.000	412.4 Da LogP 1.71 TPSA 141.4	✓ Ro5	Alert	`CC[C@@]1(O)C[C@H](O)c2c(cc3c(c2O)C(=O)c2c(O)ccc…`
ZINC2112807199 ZINC	0.875	412.4 Da LogP 1.71 TPSA 141.4	✓ Ro5	Alert	`CC[C@]1(O)C[C@@H](O)c2cc3c(c(O)c2[C@H]1C(=O)OC)…`
ZINC2112807200 ZINC	0.875	412.4 Da LogP 1.71 TPSA 141.4	✓ Ro5	Alert	`CC[C@]1(O)C[C@H](O)c2cc3c(c(O)c2[C@@H]1C(=O)OC)…`
ZINC2112807201 ZINC	0.875	412.4 Da LogP 1.71 TPSA 141.4	✓ Ro5	Alert	`CC[C@]1(O)C[C@@H](O)c2cc3c(c(O)c2[C@@H]1C(=O)OC…`
ZINC2112807202 ZINC	0.875	412.4 Da LogP 1.71 TPSA 141.4	✓ Ro5	Alert	`CC[C@]1(O)C[C@H](O)c2cc3c(c(O)c2[C@H]1C(=O)OC)C…`
ZINC102100703 ZINC	0.836	396.4 Da LogP 2.00 TPSA 121.1	✓ Ro5	Alert	`CC[C@]1(O)C[C@@H](O)c2c(cc3c(c2O)C(=O)c2ccccc2C…`
ZINC102100711 ZINC	0.836	396.4 Da LogP 2.00 TPSA 121.1	✓ Ro5	Alert	`CC[C@]1(O)C[C@H](O)c2c(cc3c(c2O)C(=O)c2ccccc2C3…`
ZINC6667726 ZINC	0.836	396.4 Da LogP 2.00 TPSA 121.1	✓ Ro5	Alert	`CC[C@]1(O)C[C@H](O)c2c(cc3c(c2O)C(=O)c2ccccc2C3…`
ZINC6667728 ZINC	0.836	396.4 Da LogP 2.00 TPSA 121.1	✓ Ro5	Alert	`CC[C@]1(O)C[C@@H](O)c2c(cc3c(c2O)C(=O)c2ccccc2C…`
ZINC3850719 ZINC	0.789	398.4 Da LogP 1.32 TPSA 141.4	✓ Ro5	Alert	`COC(=O)[C@@H]1c2cc3c(c(O)c2[C@@H](O)C[C@@]1(C)O…`
ZINC5218088 ZINC	0.772	428.4 Da LogP 1.41 TPSA 161.6	✓ Ro5	Alert	`CC[C@]1(O)C[C@H](O)c2c(O)c3c(c(O)c2[C@@H]1C(=O)…`
ZINC5218089 ZINC	0.772	428.4 Da LogP 1.41 TPSA 161.6	✓ Ro5	Alert	`CC[C@@]1(O)C[C@H](O)c2c(O)c3c(c(O)c2[C@@H]1C(=O…`
ZINC5218090 ZINC	0.772	428.4 Da LogP 1.41 TPSA 161.6	✓ Ro5	Alert	`CC[C@]1(O)C[C@@H](O)c2c(O)c3c(c(O)c2[C@@H]1C(=O…`
ZINC5218091 ZINC	0.772	428.4 Da LogP 1.41 TPSA 161.6	✓ Ro5	Alert	`CC[C@@]1(O)C[C@@H](O)c2c(O)c3c(c(O)c2[C@@H]1C(=…`
ZINC239025564 ZINC	0.634	695.8 Da LogP 3.63 TPSA 195.0	2 viol.	Alert	`CO[C@@H]1/C=C/O[C@@]2(C)Oc3c(C)c(O)c4c(c3C2=O)C…`
ZINC239025565 ZINC	0.634	695.8 Da LogP 3.63 TPSA 195.0	2 viol.	Alert	`CO[C@@H]1/C=C/O[C@@]2(C)Oc3c(C)c(O)c4c(c3C2=O)C…`
ZINC239025566 ZINC	0.634	695.8 Da LogP 3.63 TPSA 195.0	2 viol.	Alert	`CO[C@@H]1/C=C/O[C@@]2(C)Oc3c(C)c(O)c4c(c3C2=O)C…`
ZINC239025567 ZINC	0.634	695.8 Da LogP 3.63 TPSA 195.0	2 viol.	Alert	`CO[C@@H]1/C=C/O[C@@]2(C)Oc3c(C)c(O)c4c(c3C2=O)C…`
ZINC2048392601 ZINC	0.587	442.4 Da LogP 0.59 TPSA 178.7	✓ Ro5	Alert	`COC(=O)[C@H]1c2c(O)c3c(c(O)c2[C@H](O)C[C@]1(O)C…`
ZINC239229132 ZINC	0.571	811.9 Da LogP 3.16 TPSA 217.0	2 viol.	Alert	`CC[C@]1(O)C[C@H](O[C@@H]2C[C@H](N(C)C)[C@H](O[C…`
ZINC239229133 ZINC	0.571	811.9 Da LogP 3.16 TPSA 217.0	2 viol.	Alert	`CC[C@]1(O)C[C@H](O[C@@H]2C[C@H](N(C)C)[C@H](O[C…`
ZINC239229134 ZINC	0.571	811.9 Da LogP 3.16 TPSA 217.0	2 viol.	Alert	`CC[C@]1(O)C[C@H](O[C@@H]2C[C@H](N(C)C)[C@H](O[C…`

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.