KpKP13 Protein target profile

putative lactonase

Accession: KP13_05543

Gene: AHE44549.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GTN2

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Length 264

Pocket druggability (P2Rank · AlphaFold DB model) 0.848

Direct ligand evidence 0 58 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

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Moderate predicted binding pocket FPocket selected-pocket score 0.67. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.85. 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: No hit
Gut microbiome similarity: 0.2% 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.

Structure confidence

ColabFold pLDDT: 97.68 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) 0.848

Structure A0A0H3GTN2

Pocket Pocket 1

Druggability (FPocket) 0.667

Structure A0A0H3GTN2

Pocket Pocket 2

ColabFold model

P2Rank 0.774 · Pocket 1

FPocket 0.546 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 8 / 4744 genomes with a hit

Prevalence 0.2%

Sequence

Primary amino-acid sequence viewer.

MMPEIKLFMFQSGTQHCRYQHIRMNQGVGEHYEIPVPWFLLTHPDGFTLIDGGLAVEGLKDPSGYWGSAVEQFKPVMSEEQGCVEQLKRIGIAPEDIRYVVLSHLHSDHTGAIGRFPHATHVVQRQEYEYAFAPDWFTSGAYCRRDFDRPQLNWLFLNGLSDDHYDLYGDGTLQCIFTPGHSPGHQSFLIRLPGGTNFTLAIDAAYTLDHYHEKALPGLMTSATDVAQSVRKLRQLTERYHAVFIPGHDPEEWKKNRLAPACYY

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Subcellular localization

Localization: Unknown

Gene Ontology (GO)

GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

10 records

Show feature table

Start	End	DB	Term	Name
6	250	CDD	cd07729	AHL_lactonase_MBL-fold
35	248	SMART	SM00849	Lactamase_B_5a
35	248	InterPro	IPR001279	Metallo-beta-lactamase
2	264	Gene3D	G3DSA:3.60.15.10	-
2	264	InterPro	IPR036866	Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
3	256	PANTHER	PTHR42978	QUORUM-QUENCHING LACTONASE YTNP-RELATED-RELATED
34	248	Pfam	PF00753	Metallo-beta-lactamase superfamily
34	248	InterPro	IPR001279	Metallo-beta-lactamase
33	253	SUPERFAMILY	SSF56281	Metallo-hydrolase/oxidoreductase
33	253	InterPro	IPR036866	Ribonuclease Z/Hydroxyacylglutathione hydrolase-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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1

0.848

Likely same site as FPocket 1 2.6 Å 16 shared residues 89% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.035

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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #2

0.667 Unusual size

Likely same site as P2Rank 1 4.8 Å 10 shared residues 67% of smaller site

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Surrounding area

Pocket 2 FPocket #1

0.362

Likely same site as P2Rank 1 2.6 Å 16 shared residues 89% of smaller site

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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1

0.546

Likely same site as P2Rank 1 2.6 Å 12 shared residues 86% of smaller site

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Surrounding area

Pocket 2 FPocket #2

0.533

Show in viewer

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_A0A0H3GTN2	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_05543	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.

58 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 8 records from similar proteins

Structural ligands 8 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

1K4 PDB via homolog 273.4 Da · LogP 2.08 · TPSA 86.6 Open detail RCSB PDB

5PN PDB via homolog Detail RCSB PDB

C6L PDB via homolog Detail RCSB PDB

CYK PDB via homolog Detail RCSB PDB

HED 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
1K4 RCSB PDB	4J5H	A3FJ64	273.4 Da LogP 2.08 TPSA 86.6	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)N[C@@H](CCO)C(=O)O`
5PN RCSB PDB	4KEQ	Q988B9	165.1 Da LogP 0.77 TPSA 59.4	✓ Ro5	✓ Clean	`Cc1c(c2c(cn1)C(=O)OC2)O`
C6L RCSB PDB	3DHA	P0CJ63	217.3 Da LogP 0.52 TPSA 86.6	✓ Ro5	✓ Clean	`CCCCCC(=O)N[C@@H](CCO)C(=O)O`
CYK RCSB PDB	3DHC	P0CJ63	233.3 Da LogP 1.46 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCC(=O)N[C@@H](CCS)C(=O)O`
HED RCSB PDB	5EH9	P0CJ63	154.3 Da LogP 0.35 TPSA 40.5	✓ Ro5	✓ Clean	`C(CSSCCO)O`
HL4 RCSB PDB	6N9Q	A0A023DFE8	171.2 Da LogP 0.22 TPSA 55.4	✓ Ro5	✓ Clean	`CCCC(=O)N[C@H]1CCOC1=O`
HL6 RCSB PDB	6CGZ	T0BMH6	199.2 Da LogP 1.00 TPSA 55.4	✓ Ro5	✓ Clean	`CCCCCC(=O)N[C@H]1CCOC1=O`
OHN RCSB PDB	6N9R	A0A023DFE8	297.4 Da LogP 2.52 TPSA 72.5	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CC(=O)N[C@H]1CCOC1=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
ZINC137084239 ZINC	1.000	353.5 Da LogP 4.08 TPSA 72.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)CC(=O)N[C@H]1CCOC1=O`
ZINC13350890 ZINC	0.971	213.3 Da LogP 1.39 TPSA 55.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)N[C@@H]1CCOC1=O`
ZINC136677465 ZINC	0.971	241.3 Da LogP 2.17 TPSA 55.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)N[C@@H]1CCOC1=O`
ZINC4102234 ZINC	0.971	213.3 Da LogP 1.39 TPSA 55.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)N[C@H]1CCOC1=O`
ZINC43617550 ZINC	0.971	227.3 Da LogP 1.78 TPSA 55.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)N[C@H]1CCOC1=O`
ZINC62235613 ZINC	0.971	227.3 Da LogP 1.78 TPSA 55.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)N[C@@H]1CCOC1=O`
ZINC64857990 ZINC	0.971	241.3 Da LogP 2.17 TPSA 55.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)N[C@H]1CCOC1=O`
ZINC64859423 ZINC	0.846	337.5 Da LogP 4.68 TPSA 55.4	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCCC(=O)N[C@H]1CCOC1=O`
ZINC45789166 ZINC	0.842	255.3 Da LogP 1.35 TPSA 72.5	✓ Ro5	✓ Clean	`CCCCCC(=O)CCC(=O)N[C@H]1CCOC1=O`
ZINC4102231 ZINC	0.816	241.3 Da LogP 0.96 TPSA 72.5	✓ Ro5	✓ Clean	`CCCCCC(=O)CC(=O)N[C@H]1CCOC1=O`
ZINC6397039 ZINC	0.816	241.3 Da LogP 0.96 TPSA 72.5	✓ Ro5	✓ Clean	`CCCCCC(=O)CC(=O)N[C@@H]1CCOC1=O`
ZINC27647307 ZINC	0.800	309.5 Da LogP 3.90 TPSA 55.4	✓ Ro5	✓ Clean	`CCCC/C=C\CCCCCCCC(=O)N[C@H]1CCOC1=O`
ZINC135816904 ZINC	0.795	269.3 Da LogP 1.74 TPSA 72.5	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CC(=O)N[C@@H]1CCOC1=O`
ZINC137084200 ZINC	0.795	353.5 Da LogP 4.08 TPSA 72.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)CC(=O)N[C@@H]1CCOC1=O`
ZINC38146039 ZINC	0.795	283.4 Da LogP 2.13 TPSA 72.5	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CC(=O)N[C@H]1CCOC1=O`
ZINC38146043 ZINC	0.795	325.4 Da LogP 3.30 TPSA 72.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)CC(=O)N[C@H]1CCOC1=O`
ZINC42764477 ZINC	0.795	269.3 Da LogP 1.74 TPSA 72.5	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CC(=O)N[C@H]1CCOC1=O`
ZINC42804658 ZINC	0.795	325.4 Da LogP 3.30 TPSA 72.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)CC(=O)N[C@@H]1CCOC1=O`
ZINC8436849 ZINC	0.795	297.4 Da LogP 2.52 TPSA 72.5	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CC(=O)N[C@@H]1CCOC1=O`
ZINC8436851 ZINC	0.795	297.4 Da LogP 2.52 TPSA 72.5	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CC(=O)N[C@H]1CCOC1=O`
ZINC1595635455 ZINC	0.765	245.3 Da LogP 1.30 TPSA 86.6	✓ Ro5	✓ Clean	`CCCC[C@H](NC(=O)CCCCCO)C(=O)O`
ZINC83811844 ZINC	0.757	229.2 Da LogP 0.06 TPSA 92.7	✓ Ro5	✓ Clean	`O=C(O)CCCCC(=O)N[C@H]1CCOC1=O`
ZINC28537991 ZINC	0.735	357.5 Da LogP 4.12 TPSA 103.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)N[C@@H](CCC(=O)O)C(=O)O`
ZINC28538229 ZINC	0.735	385.5 Da LogP 4.90 TPSA 103.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)N[C@@H](CCC(=O)O)C(=O)O`
ZINC28538236 ZINC	0.735	385.5 Da LogP 4.90 TPSA 103.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)N[C@H](CCC(=O)O)C(=O)O`
ZINC28539035 ZINC	0.735	329.4 Da LogP 3.34 TPSA 103.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)N[C@@H](CCC(=O)O)C(=O)O`
ZINC28539044 ZINC	0.735	301.4 Da LogP 2.56 TPSA 103.7	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)N[C@@H](CCC(=O)O)C(=O)O`
ZINC28539067 ZINC	0.735	273.3 Da LogP 1.78 TPSA 103.7	✓ Ro5	✓ Clean	`CCCCCCCC(=O)N[C@@H](CCC(=O)O)C(=O)O`
ZINC390222946 ZINC	0.735	231.3 Da LogP 0.91 TPSA 86.6	✓ Ro5	✓ Clean	`CCC[C@H](NC(=O)CCCCCO)C(=O)O`
ZINC43617576 ZINC	0.735	301.4 Da LogP 2.56 TPSA 103.7	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)N[C@H](CCC(=O)O)C(=O)O`
ZINC85808238 ZINC	0.735	329.4 Da LogP 3.34 TPSA 103.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)N[C@H](CCC(=O)O)C(=O)O`
ZINC100951872 ZINC	0.727	287.4 Da LogP 2.47 TPSA 86.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)N[C@H](CO)C(=O)O`
ZINC28538025 ZINC	0.727	343.5 Da LogP 4.03 TPSA 86.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)N[C@@H](CO)C(=O)O`
ZINC28538031 ZINC	0.727	343.5 Da LogP 4.03 TPSA 86.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)N[C@H](CO)C(=O)O`
ZINC28539016 ZINC	0.727	287.4 Da LogP 2.47 TPSA 86.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)N[C@@H](CO)C(=O)O`
ZINC28539092 ZINC	0.727	315.5 Da LogP 3.25 TPSA 86.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)N[C@@H](CO)C(=O)O`
ZINC64859369 ZINC	0.727	351.5 Da LogP 3.85 TPSA 72.5	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCC(=O)CC(=O)N[C@H]1CCOC1=O`
ZINC2472231 ZINC	0.719	201.3 Da LogP 1.55 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCC(=O)N[C@@H](CC)C(=O)O`
ZINC2472233 ZINC	0.719	201.3 Da LogP 1.55 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCC(=O)N[C@H](CC)C(=O)O`
ZINC59124892 ZINC	0.718	213.2 Da LogP 0.18 TPSA 72.5	✓ Ro5	✓ Clean	`O=CCCCCC(=O)N[C@H]1CCOC1=O`
ZINC100951866 ZINC	0.697	285.4 Da LogP 3.89 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)N[C@@H](CC)C(=O)O`
ZINC22017895 ZINC	0.697	231.2 Da LogP 0.61 TPSA 103.7	✓ Ro5	✓ Clean	`CCCCCC(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC22017899 ZINC	0.697	231.2 Da LogP 0.61 TPSA 103.7	✓ Ro5	✓ Clean	`CCCCCC(=O)N[C@H](CC(=O)O)C(=O)O`
ZINC91297097 ZINC	0.697	285.4 Da LogP 3.89 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)N[C@H](CC)C(=O)O`
ZINC100654638 ZINC	0.694	328.5 Da LogP 2.74 TPSA 109.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)N[C@H](CCC(N)=O)C(=O)O`
ZINC141957116 ZINC	0.694	342.5 Da LogP 4.00 TPSA 92.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)N[C@@H](CCCN)C(=O)O`
ZINC28539029 ZINC	0.694	328.5 Da LogP 2.74 TPSA 109.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)N[C@@H](CCC(N)=O)C(=O)O`
ZINC5510744 ZINC	0.694	247.4 Da LogP 1.89 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCC(=O)N[C@H](CCSC)C(=O)O`
ZINC77286434 ZINC	0.694	300.4 Da LogP 1.96 TPSA 109.5	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)N[C@@H](CCC(N)=O)C(=O)O`
ZINC78044048 ZINC	0.694	342.5 Da LogP 4.00 TPSA 92.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)N[C@H](CCCN)C(=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.

Cross-references

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

Sequence

UniProt A0A0H3GTN2