Protein target profile

KP13_04823

Yersiniabactin biosynthesis thioesterase

Genome: KpKP13 Gene: AHE43790.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GV22

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Length 262

Pocket druggability 0.992

Direct ligand evidence 0 38 total records

Functional annotation 0 EC 2 GO

Target summary

Promising target candidate with multiple supporting evidence streams.

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 0.99, P2Rank 0.93). Use the 3D pocket comparison to verify whether they identify the same site. Strong predicted binding pocket FPocket selected-pocket score 0.99. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.93. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.

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 (%): 27.5 Lower values reduce human off-target concern.
Human E-value: 4.28e-10
Gut microbiome similarity: 0.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 44.033 Higher values support similarity to known essential genes.
DEG E-value: 1.6e-58 Smaller values mean stronger essential-gene similarity.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 94.15 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 0.992

Structure A0A0H3GV22

Pocket Pocket 1

P2Rank 0.926

Structure A0A0H3GV22

Pocket Pocket 1

ColabFold model

FPocket 0.975 · Pocket 1

P2Rank 0.908 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 4 / 4744 genomes with a hit

Prevalence 0.1%

Cross-references

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

Sequence

UniProt A0A0H3GV22

Sequence

Primary amino-acid sequence viewer.

MCIPLWPARNGNTAHLVMCPFAGGSSSAFRHWQAEQLADCALSLVTWPGRDRLRHLEPLRSITQLAALLANELEASVSPDTPLLLAGHSMGAQVAFETCRLLEQRGLAPQGLIISGCHAPHLHSERQLSHRDDADFIAELIDIGGCSPELRENQELMSLFLPLLRADFYATESYHYDSPDVCPPLRTPALLLCGSHDREASWQQVDAWRQWLSHVTGPVVIDGDHFYPIQQARSFFTQIVRHFPHAFSAMTALQKQPSTSER

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
GO:0008610 The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

9 records

Show feature table

Start	End	DB	Term	Name
12	243	PANTHER	PTHR11487	THIOESTERASE
12	243	InterPro	IPR012223	Thioesterase type II, NRPS/PKS/S-FAS
15	245	Pfam	PF00975	Thioesterase domain
15	245	InterPro	IPR001031	Thioesterase
5	241	SUPERFAMILY	SSF53474	alpha/beta-Hydrolases
5	241	InterPro	IPR029058	Alpha/Beta hydrolase fold
6	239	Gene3D	G3DSA:3.40.50.1820	alpha/beta hydrolase
6	239	InterPro	IPR029058	Alpha/Beta hydrolase fold
3	239	FunFam	G3DSA:3.40.50.1820:FF:000169	Yersiniabactin biosynthesis thioesterase YbtT

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

0.992

Likely same site as P2Rank 1 1.5 Å 22 shared residues 81% of smaller site

Unusual size

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Surrounding area

Site 2 FPocket #17

0.599

Likely same site as P2Rank 2 2.4 Å 16 shared residues 100% 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

0.926

Likely same site as FPocket 1 1.5 Å 22 shared residues 81% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.583

Likely same site as FPocket 17 2.4 Å 16 shared residues 100% of smaller site

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Surrounding area

Site 3 P2Rank #3

0.088

Likely same site as FPocket 17 4.7 Å 10 shared residues 91% 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

0.908

Likely same site as FPocket 1 1.5 Å 26 shared residues 90% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.135

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Surrounding area

Site 3 P2Rank #3

0.067

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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_A0A0H3GV22	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_04823	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.

38 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 1 records from similar proteins

Structural ligands 1 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 37 similarity-based ZINC candidates

Best available ligand signal

E9H PDB via homolog 322.4 Da · LogP 5.58 · TPSA 66.8 Open detail RCSB PDB

ZINC1673633 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC1849859 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC2038200 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC2522710 ZINC proposed compound · Tanimoto 0.708 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
E9H RCSB PDB	6FVJ	P9WQD5	322.4 Da LogP 5.58 TPSA 66.8	1 viol.	✓ Clean	`CCCCCCCCCCCCCCCCOP(=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
ZINC1673633 ZINC	1.000	266.3 Da LogP 4.02 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOP(=O)(O)O`
ZINC1849859 ZINC	1.000	238.3 Da LogP 3.24 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCCCOP(=O)(O)O`
ZINC2038200 ZINC	1.000	210.2 Da LogP 2.46 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCOP(=O)(O)O`
ZINC2522710 ZINC	0.708	238.3 Da LogP 3.50 TPSA 55.8	✓ Ro5	✓ Clean	`CCCCCOP(=O)(O)OCCCCC`
ZINC44630076 ZINC	0.615	284.4 Da LogP 3.54 TPSA 66.8	✓ Ro5	✓ Clean	`O=P(O)(O)OCCCCCCCCCCCS`
ZINC2545285 ZINC	0.607	210.2 Da LogP 2.31 TPSA 66.8	✓ Ro5	✓ Clean	`CC(C)CCCCCOP(=O)(O)O`
ZINC1577196 ZINC	0.600	210.2 Da LogP 2.72 TPSA 55.8	✓ Ro5	✓ Clean	`CCCCOP(=O)(O)OCCCC`
ZINC59303553 ZINC	0.594	396.5 Da LogP 4.95 TPSA 96.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCCOC[C@H](O)COP(=O)(O)O`
ZINC59303559 ZINC	0.594	396.5 Da LogP 4.95 TPSA 96.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCCOC[C@@H](O)COP(=O)(O)O`
ZINC4952299 ZINC	0.593	238.3 Da LogP 3.76 TPSA 44.8	✓ Ro5	✓ Clean	`CCCCCCOP(=O)(OCC)OCC`
ZINC113027531 ZINC	0.581	310.4 Da LogP 3.58 TPSA 55.8	✓ Ro5	✓ Clean	`CCCCCCCCCO[P@](=O)(O)OCC[N+](C)(C)C`
ZINC217410460 ZINC	0.581	338.4 Da LogP 4.36 TPSA 55.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCO[P@@](=O)(O)OCC[N+](C)(C)C`
ZINC3649862 ZINC	0.581	296.4 Da LogP 3.19 TPSA 55.8	✓ Ro5	✓ Clean	`CCCCCCCCO[P@](=O)(O)OCC[N+](C)(C)C`
ZINC43562168 ZINC	0.581	352.5 Da LogP 4.75 TPSA 55.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCO[P@@](=O)(O)OCC[N+](C)(C)C`
ZINC58660415 ZINC	0.581	324.4 Da LogP 3.97 TPSA 55.8	✓ Ro5	✓ Clean	`CCCCCCCCCCO[P@@](=O)(O)OCC[N+](C)(C)C`
ZINC1737261 ZINC	0.577	237.3 Da LogP 3.47 TPSA 61.5	✓ Ro5	✓ Clean	`CCCCCOP(N)(=O)OCCCCC`
ZINC139175830 ZINC	0.576	379.5 Da LogP 4.69 TPSA 95.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)NCCOP(=O)(O)O`
ZINC1583715 ZINC	0.533	232.3 Da LogP 2.32 TPSA 32.3	✓ Ro5	✓ Clean	`CCCCCCOP(=O)(N1CC1)N1CC1`
ZINC1681795 ZINC	0.533	260.3 Da LogP 3.10 TPSA 32.3	✓ Ro5	✓ Clean	`CCCCCCCCOP(=O)(N1CC1)N1CC1`
ZINC5158188 ZINC	0.531	322.3 Da LogP 3.34 TPSA 93.1	✓ Ro5	✓ Clean	`C=C(C)C(=O)OCCCCCCCCCCOP(=O)(O)O`
ZINC1586777 ZINC	0.520	266.3 Da LogP 4.54 TPSA 44.8	✓ Ro5	✓ Clean	`CCCCOP(=O)(OCCCC)OCCCC`
ZINC1718616 ZINC	0.519	201.3 Da LogP 3.22 TPSA 52.3	✓ Ro5	✓ Clean	`CCCCCCCCCCOC(N)=O`
ZINC1865453 ZINC	0.519	229.4 Da LogP 4.00 TPSA 52.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOC(N)=O`
ZINC4833922 ZINC	0.517	366.2 Da LogP 3.18 TPSA 130.4	✓ Ro5	✓ Clean	`CCCCO[P@](=O)(O)CP(=O)(O)C[P@@](=O)(O)OCCCC`
ZINC102192623 ZINC	0.500	367.5 Da LogP 3.88 TPSA 113.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[C@@H](O)[C@@H](N)COP(=O)(O)O`
ZINC1600124 ZINC	0.500	222.3 Da LogP 3.30 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCCCP(=O)(O)O`
ZINC1600143 ZINC	0.500	250.3 Da LogP 4.09 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCP(=O)(O)O`
ZINC16052649 ZINC	0.500	419.4 Da LogP 4.87 TPSA 115.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[P+](C)(C)CC(P(=O)(O)O)P(=O)(O)O`
ZINC1678069 ZINC	0.500	224.2 Da LogP 2.76 TPSA 55.8	✓ Ro5	✓ Clean	`CCCCOP(=O)(CO)OCCCC`
ZINC2023373 ZINC	0.500	234.3 Da LogP 4.42 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCP(=O)(O)CCCCCC`
ZINC2038652 ZINC	0.500	208.2 Da LogP 3.44 TPSA 35.5	✓ Ro5	✓ Clean	`CCCCOP(C)(=O)OCCCC`
ZINC36178975 ZINC	0.500	278.4 Da LogP 4.87 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCP(=O)(O)O`
ZINC59393630 ZINC	0.500	252.2 Da LogP 1.39 TPSA 93.1	✓ Ro5	✓ Clean	`C=CC(=O)OCCCCCCOP(=O)(O)O`
ZINC60139895 ZINC	0.500	222.3 Da LogP 3.53 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCCCCCCO[P@@H](=O)O`
ZINC8216762 ZINC	0.500	381.5 Da LogP 4.27 TPSA 113.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC[C@H](O)[C@H](N)COP(=O)(O)O`
ZINC97976220 ZINC	0.500	208.2 Da LogP 2.91 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCCP(=O)(O)O`
ZINC97976221 ZINC	0.500	236.3 Da LogP 3.69 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCP(=O)(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.