KpATCC43816 Protein target profile

proofreading thioesterase in enterobactin biosynthesis

Accession: VK055_0301

Gene: AIK78927.1 ybdB 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GUW6

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Length 136

Pocket druggability (FPocket · AlphaFold DB model) 0.273

Metabolic reactions 1

Chokepoint No

Direct ligand evidence 0 59 total records

Functional annotation 1 EC 3 GO

Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 9 structural and 0 bioactivity records.

Risks to review

Microbiome similarity 162 of 4744 screened genomes (3.4%) have a significant similarity hit. Mixed conservation Core/accessory calls are not fully concordant. Weak predicted binding pocket FPocket selected-pocket score 0.27.

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: 3.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 82.353 Higher values support similarity to known essential genes.
DEG E-value: 6.09e-85 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 97.98 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)

Structure A0A0H3GUW6

Pocket No pockets

Druggability (FPocket) 0.273

Structure A0A0H3GUW6

Pocket Pocket 1

ColabFold model

FPocket 0.172 · Pocket 3

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 162 / 4744 genomes with a hit

Prevalence 3.4%

Metabolic context

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

Explore metabolic network

Metabolic context: no human homolog detected.

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

Chokepoint Not a chokepoint

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MIWKRQATLEQLNRLGDGNMVGLLDIRFETVTDDTLEATMPVDSRTQQPFGLLHGGASVVLAETLGSVAGYLCSEGEQKVVGLEVNANHIRSARGGRVRGVCKALHVGTRHQVWQIEIFDEQSRLCCSSRLTTAVI

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Subcellular localization

Localization: Unknown

Enzyme Commission (EC)

3.1.2.28

Gene Ontology (GO)

GO:0061522 Catalysis of the reaction 1,4-dihydroxy-2-naphthoyl-CoA + H2O = 1,4-dihydroxy-2-naphthoate + CoA + H+.
GO:0009234 The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

12 records

Show feature table

Start	End	DB	Term	Name
20	135	NCBIfam	TIGR00369	hotdog fold thioesterase
20	135	InterPro	IPR003736	Phenylacetic acid degradation-related domain
1	136	FunFam	G3DSA:3.10.129.10:FF:000002	1,4-dihydroxy-2-naphthoyl-CoA hydrolase
18	133	PANTHER	PTHR43240	1,4-DIHYDROXY-2-NAPHTHOYL-COA THIOESTERASE 1
50	127	Pfam	PF03061	Thioesterase superfamily
50	127	InterPro	IPR006683	Thioesterase domain
1	136	Hamap	MF_01936	1,4-dihydroxy-2-naphthoyl-CoA hydrolase [menI].
1	136	InterPro	IPR030863	1,4-dihydroxy-2-naphthoyl-CoA hydrolase, MenI
1	133	SUPERFAMILY	SSF54637	Thioesterase/thiol ester dehydrase-isomerase
1	133	InterPro	IPR029069	HotDog domain superfamily
23	135	CDD	cd03443	PaaI_thioesterase
1	136	Gene3D	G3DSA:3.10.129.10	Hotdog Thioesterase

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

Pocket 1 FPocket #1

0.273

Show in viewer

Surrounding area

Residue sets

UniProt: Active site:63-63 Nucleophile or proton acceptor

UniProt: Binding site:106-111

UniProt: Binding site:82-82

UniProt: Binding site:89-92

Residue sets

UniProt: Active site:63-63 Nucleophile or proton acceptor

UniProt: Binding site:106-111

UniProt: Binding site:82-82

UniProt: Binding site:89-92

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_A0A0H3GUW6	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_0301	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.

59 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 9 records from similar proteins

Structural ligands 9 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

0FQ PDB via homolog 885.7 Da · LogP 0.02 · TPSA 363.6 Open detail RCSB PDB

31B PDB via homolog Detail RCSB PDB

4CA PDB via homolog Detail RCSB PDB

4CO PDB via homolog Detail RCSB PDB

5NE 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
0FQ RCSB PDB	4K4C	P0A8Y8	885.7 Da LogP 0.02 TPSA 363.6	3 viol.	✓ Clean	`CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H](…`
31B RCSB PDB	4QD9	Q9I3A4	775.6 Da LogP -0.79 TPSA 337.2	3 viol.	✓ Clean	`CC(C)(COP(=O)(O)OP(=O)(O)OC[C@H]1[C@H]([C@H]([C…`
4CA RCSB PDB	1Q4U	Q04416	873.7 Da LogP 0.04 TPSA 366.8	3 viol.	✓ Clean	`CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H](…`
4CO RCSB PDB	1Q4T	Q04416	901.7 Da LogP -0.27 TPSA 383.9	3 viol.	✓ Clean	`CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H](…`
5NE RCSB PDB	5HMC	B4XYA6	186.2 Da LogP 2.85 TPSA 37.3	✓ Ro5	✓ Clean	`Cc1cccc2c1cccc2C(=O)O`
HFQ RCSB PDB	4K4D	P0A8Y8	917.7 Da LogP -0.57 TPSA 404.1	3 viol.	✓ Clean	`CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H](…`
MLI RCSB PDB	4K4D	P0A8Y8	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(=O)[O-]`
PHB RCSB PDB	1Q4S	Q04416	138.1 Da LogP 1.09 TPSA 57.5	✓ Ro5	✓ Clean	`c1cc(ccc1C(=O)O)O`
UOQ RCSB PDB	4K4B	P77781	935.8 Da LogP 1.85 TPSA 363.6	3 viol.	✓ Clean	`CCCCCCCCCC(=O)CSCCNC(=O)CCNC(=O)[C@@H](C(C)(C)C…`

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
ZINC389804 ZINC	0.842	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(O)cc2)cc1`
ZINC45070868 ZINC	0.739	216.2 Da LogP 2.24 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1cccc2c(C(=O)O)cccc12`
ZINC33246180 ZINC	0.727	242.2 Da LogP 3.51 TPSA 82.2	✓ Ro5	Alert	`O=C(O)c1ccc(N=Nc2ccc(O)cc2)cc1`
ZINC3896282 ZINC	0.727	242.2 Da LogP 3.51 TPSA 82.2	✓ Ro5	Alert	`O=C(O)c1ccc(/N=N/c2ccc(O)cc2)cc1`
ZINC392302 ZINC	0.727	230.2 Da LogP 2.88 TPSA 66.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(O)cc2)cc1`
ZINC289893 ZINC	0.696	278.3 Da LogP 1.92 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(S(=O)(=O)c2ccc(O)cc2)cc1`
ZINC114185151 ZINC	0.667	298.2 Da LogP 2.15 TPSA 108.7	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC2924369 ZINC	0.667	242.2 Da LogP 2.16 TPSA 74.6	✓ Ro5	Alert	`O=C(C(=O)c1ccc(O)cc1)c1ccc(O)cc1`
ZINC3156317 ZINC	0.640	258.2 Da LogP 2.31 TPSA 83.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(OC(=O)c2ccc(O)cc2)cc1`
ZINC4903179 ZINC	0.640	257.2 Da LogP 2.34 TPSA 86.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(NC(=O)c2ccc(O)cc2)cc1`
ZINC34454555 ZINC	0.633	200.2 Da LogP 2.93 TPSA 26.3	✓ Ro5	✓ Clean	`COC(=O)c1cccc2c(C)cccc12`
ZINC134079 ZINC	0.632	242.2 Da LogP 2.75 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)cc2)cc1`
ZINC1640789 ZINC	0.632	374.3 Da LogP 3.55 TPSA 108.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccc(C(=O)c3ccc(C(=O)O)cc3)cc…`
ZINC2146859 ZINC	0.632	270.2 Da LogP 2.31 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC28449 ZINC	0.632	214.2 Da LogP 2.33 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(c1ccc(O)cc1)c1ccc(O)cc1`
ZINC3147211 ZINC	0.632	318.3 Da LogP 4.42 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccc(C(=O)O)cc3)cc2)cc1`
ZINC332365 ZINC	0.632	318.3 Da LogP 3.56 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(c1ccc(O)cc1)c1ccc(C(=O)c2ccc(O)cc2)cc1`
ZINC1713131 ZINC	0.630	270.3 Da LogP 3.37 TPSA 74.6	✓ Ro5	✓ Clean	`Cc1cccc(C(=O)O)c1-c1c(C)cccc1C(=O)O`
ZINC75618817 ZINC	0.625	210.2 Da LogP 1.16 TPSA 83.8	✓ Ro5	✓ Clean	`Cc1cccc(C(=O)O)c1OCC(=O)O`
ZINC1705144 ZINC	0.619	226.2 Da LogP 2.46 TPSA 54.4	✓ Ro5	Alert	`O=C(C(=O)c1ccc(O)cc1)c1ccccc1`
ZINC404239 ZINC	0.607	262.0 Da LogP 2.30 TPSA 37.3	✓ Ro5	✓ Clean	`Cc1cccc(C(=O)O)c1I`
ZINC108270626 ZINC	0.600	200.2 Da LogP 3.10 TPSA 37.3	✓ Ro5	✓ Clean	`CCc1cccc2c(C(=O)O)cccc12`
ZINC141610950 ZINC	0.600	230.2 Da LogP 2.32 TPSA 63.6	✓ Ro5	✓ Clean	`COC(=O)c1cccc2c(C(=O)O)cccc12`
ZINC389564 ZINC	0.600	216.2 Da LogP 2.24 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)O)c2ccccc12`
ZINC958718003 ZINC	0.600	229.2 Da LogP 1.90 TPSA 66.4	✓ Ro5	✓ Clean	`CNC(=O)c1cccc2c(C(=O)O)cccc12`
ZINC6338454 ZINC	0.593	268.3 Da LogP 2.99 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(/C=C/C(=O)c2ccc(O)cc2)cc1`
ZINC37729611 ZINC	0.588	242.3 Da LogP 3.27 TPSA 46.5	✓ Ro5	✓ Clean	`Cc1cccc(C(=O)O)c1OCc1ccccc1`
ZINC952985963 ZINC	0.588	250.3 Da LogP 4.31 TPSA 37.3	✓ Ro5	✓ Clean	`Cc1ccc2c(C(=O)O)cc3c(C)cccc3c2c1`
ZINC34370957 ZINC	0.586	298.1 Da LogP 3.14 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1cccc2c(I)cccc12`
ZINC404236 ZINC	0.586	215.0 Da LogP 2.46 TPSA 37.3	✓ Ro5	✓ Clean	`Cc1cccc(C(=O)O)c1Br`
ZINC531346 ZINC	0.586	206.6 Da LogP 3.19 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1cccc2c(Cl)cccc12`
ZINC74123 ZINC	0.586	251.1 Da LogP 3.30 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1cccc2c(Br)cccc12`
ZINC65340137 ZINC	0.583	258.2 Da LogP 2.46 TPSA 94.8	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(=O)O)cc(-c2ccc(O)cc2)c1`
ZINC34568728 ZINC	0.581	202.2 Da LogP 2.55 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cccc2c(C(=O)O)cccc12`
ZINC167246 ZINC	0.571	248.0 Da LogP 1.99 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(I)cc1`
ZINC288837 ZINC	0.571	260.2 Da LogP 1.93 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)O)c2c(C(=O)O)cccc12`
ZINC3269660 ZINC	0.571	254.2 Da LogP 2.45 TPSA 71.4	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccccc2)cc1`
ZINC34573580 ZINC	0.571	496.5 Da LogP 4.86 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(c2ccc(C(=O)O)cc2)(c2ccc(C(=O)O)cc…`
ZINC388063 ZINC	0.571	201.0 Da LogP 2.15 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Br)cc1`
ZINC1601954 ZINC	0.567	200.2 Da LogP 2.78 TPSA 37.3	✓ Ro5	✓ Clean	`Cc1cccc2c(CC(=O)O)cccc12`
ZINC71256871 ZINC	0.567	248.3 Da LogP 4.21 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1cccc2c(-c3ccccc3)cccc12`
ZINC114966203 ZINC	0.552	214.2 Da LogP 2.74 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)c1ccc(C(=O)O)c2ccccc12`
ZINC5234593 ZINC	0.552	293.3 Da LogP 1.89 TPSA 103.7	✓ Ro5	Alert	`O=C(O)c1ccc(S(=O)(=O)Nc2ccc(O)cc2)cc1`
ZINC1871910 ZINC	0.548	222.2 Da LogP 3.69 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1cccc2c1ccc1ccccc12`
ZINC70679886 ZINC	0.548	214.2 Da LogP 2.42 TPSA 54.4	✓ Ro5	✓ Clean	`Cc1ccc(C(=O)C(=O)O)c2ccccc12`
ZINC13375284 ZINC	0.545	270.2 Da LogP 3.50 TPSA 99.3	✓ Ro5	Alert	`O=C(O)c1ccc(N=Nc2ccc(C(=O)O)cc2)cc1`
ZINC1857524265 ZINC	0.545	268.3 Da LogP 3.25 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C=Cc2ccc(C(=O)O)cc2)cc1`
ZINC188555 ZINC	0.545	350.3 Da LogP 4.67 TPSA 93.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(Oc3ccc(C(=O)O)cc3)cc2)cc1`
ZINC4309722 ZINC	0.545	270.2 Da LogP 3.50 TPSA 99.3	✓ Ro5	Alert	`O=C(O)c1ccc(/N=N/c2ccc(C(=O)O)cc2)cc1`
ZINC59301968 ZINC	0.545	394.3 Da LogP 2.54 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)c1ccc(P(c2ccc(C(=O)O)cc2)c2ccc(C(=O)O)cc2…`

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 A0A0H3GUW6

Pathways

BioCyc RXN0-7046