Protein target profile

VK055_1890

acireductone dioxygenase

Genome: KpATCC43816 Gene: mtnD AIK80496.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GTU3

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Length 180

Pocket druggability 0.91

Metabolic reactions 2

Chokepoint No

Direct ligand evidence 0 54 total records

Functional annotation 2 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

Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.91, P2Rank 0.79). Use the 3D pocket comparison to verify whether they identify the same site. Central metabolic position More central than 91.7% of genes in this genome. 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. 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 (%): 34.667 Lower values reduce human off-target concern.
Human E-value: 1.85e-07
Gut microbiome similarity: 1.7% 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: Cytoplasmic

Structure confidence

ColabFold pLDDT: 91.77 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 0.91

Structure A0A0H3GTU3

Pocket Pocket 2

P2Rank 0.79

Structure A0A0H3GTU3

Pocket Pocket 1

ColabFold model

FPocket 0.531 · Pocket 1

P2Rank 0.519 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 81 / 4744 genomes with a hit

Prevalence 1.7%

Cross-references

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

Sequence

UniProt A0A0H3GTU3

Pathways

KEGG R07364 BioCyc R147-RXN KEGG R07363 BioCyc R146-RXN

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 91.7% of genes in this genome.

Relative network centrality 91.7% more central than 91.7% of genes in this genome

Chokepoint Not a chokepoint

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSALTLFSVTDPQTPVWHSTDASAIQAQLNAKGVRFERWQADRDLGANPSPETVIAAYQHAIDKLVAEKGYQSWDVISLRADNPQKEALREKFLNEHTHGEDEVRFFVEGAGLFCLHIGDEVFQVLCEKNDLISVPAHTPHWFDMGSEPNFTAIRIFDNPEGWIAQFTGDDIASAYPRLA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 6 GO

Enzyme Commission (EC)

Gene Ontology (GO)

GO:0010308 Catalysis of the reaction: 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2 = 3-(methylthio)propanoate + CO + formate.
GO:0005506 Binding to an iron (Fe) ion.
GO:0010309 Catalysis of the reaction: 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2 = 4-methylthio-2-oxobutanoate + formate + H+.
GO:0016151 Binding to a nickel (Ni) cation.
GO:0019284 OBSOLETE. The chemical reactions and pathways resulting in the formation of L-methionine from S-adenosylmethionine.
GO:0019509 OBSOLETE. The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

12 records

Show feature table

Start	End	DB	Term	Name
4	178	SUPERFAMILY	SSF51182	RmlC-like cupins
4	178	InterPro	IPR011051	RmlC-like cupin domain superfamily
2	157	Gene3D	G3DSA:2.60.120.10	Jelly Rolls
2	157	InterPro	IPR014710	RmlC-like jelly roll fold
18	165	Pfam	PF03079	ARD/ARD' family
18	165	InterPro	IPR004313	Acireductone dioxygenase ARD family
27	165	CDD	cd02232	cupin_ARD
27	165	InterPro	IPR004313	Acireductone dioxygenase ARD family
11	170	PANTHER	PTHR23418	ACIREDUCTONE DIOXYGENASE
11	170	InterPro	IPR004313	Acireductone dioxygenase ARD family
1	172	Hamap	MF_01682	Acireductone dioxygenase [mtnD].
1	172	InterPro	IPR023956	Acireductone dioxygenase ARD, bacteria

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 #2

0.91

Likely same site as P2Rank 1 1.1 Å 15 shared residues 94% of smaller site

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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

0.79

Likely same site as FPocket 2 1.1 Å 15 shared residues 94% of smaller site

Show in viewer

Surrounding area

Residue sets

UniProt: Binding site:103-103

UniProt: Binding site:141-141

UniProt: Binding site:97-97

UniProt: Binding site:99-99

UniProt: Site:102-102 May play a role in transmitting local conformational changes

UniProt: Site:105-105 Important to generate the dianion

UniProt: Site:96-96 May play a role in metal incorporation in vivo

Residue sets

UniProt: Binding site:103-103

UniProt: Binding site:141-141

UniProt: Binding site:97-97

UniProt: Binding site:99-99

UniProt: Site:102-102 May play a role in transmitting local conformational changes

UniProt: Site:105-105 Important to generate the dianion

UniProt: Site:96-96 May play a role in metal incorporation in vivo

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_A0A0H3GTU3	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_1890	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.

54 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 4 records from similar proteins

Structural ligands 4 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

69O PDB via homolog 116.1 Da · LogP 0.44 · TPSA 54.4 Open detail RCSB PDB

KMT PDB via homolog Detail RCSB PDB

LAC PDB via homolog Detail RCSB PDB

LEA PDB via homolog Detail RCSB PDB

ZINC1529498 ZINC proposed compound · Tanimoto 0.778 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
69O RCSB PDB	5I93	Q99JT9	116.1 Da LogP 0.44 TPSA 54.4	✓ Ro5	✓ Clean	`CCCC(=O)C(=O)O`
KMT RCSB PDB	5I8Y	Q99JT9	148.2 Da LogP 0.39 TPSA 54.4	✓ Ro5	✓ Clean	`CSCCC(=O)C(=O)O`
LAC RCSB PDB	5I8T	Q99JT9	90.1 Da LogP -0.55 TPSA 57.5	✓ Ro5	✓ Clean	`C[C@H](C(=O)O)O`
LEA RCSB PDB	5I8S	Q99JT9	102.1 Da LogP 1.26 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCC(=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
ZINC1529498 ZINC	0.778	200.3 Da LogP 3.99 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)O`
ZINC1530417 ZINC	0.778	228.4 Da LogP 4.77 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)O`
ZINC1628119 ZINC	0.778	214.3 Da LogP 4.38 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)O`
ZINC2113934081 ZINC	0.750	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCCCCCC(=O)O`
ZINC2243668 ZINC	0.750	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCC(=O)O`
ZINC2378799 ZINC	0.750	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCC(=O)O`
ZINC33820423 ZINC	0.750	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCCCC(=O)O`
ZINC2378801 ZINC	0.700	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCC(=O)O`
ZINC138457918 ZINC	0.667	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCC(=O)O`
ZINC138458029 ZINC	0.667	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCC(=O)O`
ZINC144395054 ZINC	0.667	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCC(=O)O`
ZINC14619628 ZINC	0.667	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCCCC(=O)O`
ZINC196749828 ZINC	0.667	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCC(=O)O`
ZINC2113934076 ZINC	0.667	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCC(=O)O`
ZINC2113934082 ZINC	0.667	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCC(=O)O`
ZINC2113934083 ZINC	0.667	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCC(=O)O`
ZINC2243670 ZINC	0.667	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCC(=O)O`
ZINC2569203 ZINC	0.667	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCC(=O)O`
ZINC4798470 ZINC	0.667	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCCC(=O)O`
ZINC5973005 ZINC	0.667	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCC(=O)O`
ZINC71418182 ZINC	0.667	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCC(=O)CCCCC(=O)O`
ZINC79244776 ZINC	0.667	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCCC(=O)O`
ZINC86037082 ZINC	0.667	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCCC(=O)O`
ZINC86037089 ZINC	0.667	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCCCC(=O)O`
ZINC86039283 ZINC	0.667	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCC(=O)O`
ZINC11799246 ZINC	0.636	215.3 Da LogP 2.75 TPSA 40.5	✓ Ro5	✓ Clean	`CCCCN(CCCC)CCCC(=O)O`
ZINC3160730 ZINC	0.636	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCC(=O)O`
ZINC4582907 ZINC	0.636	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCC(=O)O`
ZINC4727003 ZINC	0.636	312.4 Da LogP 4.69 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCC(=O)CCCCCCCC(=O)O`
ZINC86037074 ZINC	0.636	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)CCCC(=O)O`
ZINC36923853 ZINC	0.600	201.3 Da LogP 1.50 TPSA 57.6	✓ Ro5	✓ Clean	`CCCCC(=O)N(C)CCCC(=O)O`
ZINC2113934064 ZINC	0.591	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCC(=O)CCCCCCCCCCCC(=O)O`
ZINC2113934089 ZINC	0.591	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCC(=O)CCCCCCCCCCC(=O)O`
ZINC2378809 ZINC	0.591	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCC(=O)CCCCCCC(=O)O`
ZINC1529497 ZINC	0.588	230.3 Da LogP 3.06 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCC(=O)O`
ZINC1531045 ZINC	0.588	202.2 Da LogP 2.28 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)O`
ZINC1593115 ZINC	0.588	216.3 Da LogP 2.67 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCC(=O)O`
ZINC1700020 ZINC	0.588	244.3 Da LogP 3.45 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCC(=O)O`
ZINC3860440 ZINC	0.588	258.4 Da LogP 3.84 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCC(=O)O`
ZINC3861298 ZINC	0.588	286.4 Da LogP 4.62 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCC(=O)O`
ZINC5113062 ZINC	0.588	272.4 Da LogP 4.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCC(=O)O`
ZINC1531062 ZINC	0.583	226.4 Da LogP 4.55 TPSA 37.3	✓ Ro5	✓ Clean	`CCCC/C=C/CCCCCCCC(=O)O`
ZINC1600675 ZINC	0.583	232.4 Da LogP 3.94 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCSCCCC(=O)O`
ZINC2387442 ZINC	0.583	246.4 Da LogP 4.34 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCSCCCCC(=O)O`
ZINC2504617 ZINC	0.583	240.4 Da LogP 4.94 TPSA 37.3	✓ Ro5	✓ Clean	`CCCC/C=C/CCCCCCCCC(=O)O`
ZINC28539337 ZINC	0.583	224.3 Da LogP 4.00 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCC#CCCCC(=O)O`
ZINC33822238 ZINC	0.583	210.3 Da LogP 3.61 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCC#CCCCCCCC(=O)O`
ZINC4529321 ZINC	0.583	226.4 Da LogP 4.55 TPSA 37.3	✓ Ro5	✓ Clean	`CCCC/C=C\CCCCCCCC(=O)O`
ZINC5260769 ZINC	0.583	240.4 Da LogP 4.94 TPSA 37.3	✓ Ro5	✓ Clean	`CCCC/C=C\CCCCCCCCC(=O)O`
ZINC88378988 ZINC	0.583	243.4 Da LogP 3.58 TPSA 49.3	✓ Ro5	✓ Clean	`CCCCCCCCCCNCCCC(=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.