Genome KpKP13

Protein target profile

Protein pemK

Accession: KP13_01394

Gene: AHE47436.1 pemK 3D evidence: AlphaFold DB model + ColabFold model UniProt R9R7H5

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Length 110

Pocket druggability (P2Rank) 0.007

Direct ligand evidence 0 53 total records

Functional annotation 1 EC 5 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.

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: 0.5% 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: 93.24 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) 0.007

Structure R9R7H5

Pocket Pocket 1

Druggability (FPocket) 0.053

Structure R9R7H5

Pocket Pocket 4

ColabFold model

P2Rank 0.001 · Pocket 1

FPocket 0.429 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 26 / 4744 genomes with a hit

Prevalence 0.5%

Cross-references

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

Sequence

UniProt R9R7H5

Chemistry

ChEMBL CHEMBL1324227

Sequence

Primary amino-acid sequence viewer.

MERGEIWLVSLDPTAGHEQQGTRPVLIVTPAAFNRVTRLPVVVPVTSGGNFARTAGFAVSLDGAGIRTTGVVRCDQPRTIDMKARGGKRLERVPETIMDDVLGRLATILT

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization: Unknown

Enzyme Commission (EC)

3.1.-.-

Gene Ontology (GO)

GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
GO:0004521 Catalysis of the cleavage of ester linkages within ribonucleic acid by creating internal breaks.
GO:0006402 The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
GO:0016075 The chemical reactions and pathways resulting in the breakdown of rRNA, ribosomal RNA, a structural constituent of ribosomes.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

9 records

Show feature table

Start	End	DB	Term	Name
1	109	SUPERFAMILY	SSF50118	Cell growth inhibitor/plasmid maintenance toxic component
1	110	Gene3D	G3DSA:2.30.30.110	-
1	110	InterPro	IPR011067	Plasmid maintenance toxin/Cell growth inhibitor
1	110	PIRSF	PIRSF033490	MazF
1	110	InterPro	IPR003477	mRNA interferase PemK-like
1	109	PANTHER	PTHR33988	ENDORIBONUCLEASE MAZF-RELATED
1	109	InterPro	IPR003477	mRNA interferase PemK-like
2	108	Pfam	PF02452	PemK-like, MazF-like toxin of type II toxin-antitoxin system
2	108	InterPro	IPR003477	mRNA interferase PemK-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

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1

0.007

Show in viewer

Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1

0.429

Show in viewer

Surrounding area

Pocket 2 FPocket #2

0.299

Likely same site as P2Rank 1 1.8 Å 8 shared residues 100% of smaller site

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_R9R7H5	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_01394	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.

53 records

Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records

Transferred evidence 3 records from similar proteins

Structural ligands 2 0 loaded crystals

Measured bioactivity 1 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

1PG PDB via homolog 252.3 Da · LogP -0.31 · TPSA 66.4 Open detail RCSB PDB

3PO PDB via homolog Detail RCSB PDB

CHEMBL1324227 ChEMBL via homolog · pchembl 6.57 (~269.2 nM) Detail ChEMBL

ZINC103543913 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC103543928 ZINC proposed compound · Tanimoto 1.000 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
1PG RCSB PDB	1NE8	P96622	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
3PO RCSB PDB	7D2M	Q9RX98	258.0 Da LogP -0.69 TPSA 170.8	✓ Ro5	✓ Clean	`OP(=O)(O)OP(=O)(O)OP(=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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL1324227 ChEMBL	P0AE70	6.57 ~269.2 nM	395.4 Da LogP 1.81 TPSA 115.5	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@@H]3C(C(=O)c4ccc5ccccc5n4)=N…`

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
ZINC103543913 ZINC	1.000	395.4 Da LogP 1.81 TPSA 115.5	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@@H]3C(C(=O)c4ccc5ccccc5n4)=N…`
ZINC103543928 ZINC	1.000	395.4 Da LogP 1.81 TPSA 115.5	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@H]3NN=C(C(=O)c4ccc5ccccc5n4)…`
ZINC1580161 ZINC	1.000	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16037518 ZINC	1.000	395.4 Da LogP 1.81 TPSA 115.5	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@@H]3NN=C(C(=O)c4ccc5ccccc5n4…`
ZINC16052118 ZINC	1.000	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257 ZINC	1.000	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC18202958 ZINC	1.000	395.4 Da LogP 1.81 TPSA 115.5	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@H]3NN=C(C(=O)c4ccc5ccccc5n4)…`
ZINC34317654 ZINC	1.000	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059 ZINC	1.000	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101 ZINC	1.000	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5997860 ZINC	1.000	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC6827739 ZINC	1.000	258.0 Da LogP -0.69 TPSA 170.8	✓ Ro5	✓ Clean	`O=P(O)(O)OP(=O)(O)OP(=O)(O)O`
ZINC575419714 ZINC	0.727	312.4 Da LogP 0.42 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCSCCOCCOCCO`
ZINC115163232 ZINC	0.700	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCCO`
ZINC258837490 ZINC	0.700	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCCO`
ZINC12501520 ZINC	0.688	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1692489 ZINC	0.688	222.3 Da LogP 0.33 TPSA 46.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOC`
ZINC3874716 ZINC	0.688	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769 ZINC	0.688	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548 ZINC	0.688	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC4530388 ZINC	0.688	266.3 Da LogP 0.35 TPSA 55.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOC`
ZINC5178829 ZINC	0.688	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830 ZINC	0.688	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5701172 ZINC	0.688	310.4 Da LogP 0.36 TPSA 64.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOC`
ZINC5997861 ZINC	0.688	398.5 Da LogP 0.40 TPSA 83.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOC`
ZINC6476653 ZINC	0.677	388.4 Da LogP 2.07 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(C1=NN[C@@H]2C(=O)N(c3cccc(F)c3)C(=O)[C@H]12…`
ZINC575432150 ZINC	0.667	344.4 Da LogP -0.89 TPSA 100.5	✓ Ro5	✓ Clean	`COCCOCCOCCS(=O)(=O)CCOCCOCCO`
ZINC16034323 ZINC	0.656	438.4 Da LogP 2.95 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(C1=NN[C@@H]2C(=O)N(c3cccc(C(F)(F)F)c3)C(=O)…`
ZINC17920729 ZINC	0.656	400.4 Da LogP 1.94 TPSA 101.0	✓ Ro5	✓ Clean	`COc1cccc(N2C(=O)[C@H]3NN=C(C(=O)c4ccc5ccccc5n4)…`
ZINC100671216 ZINC	0.656	346.3 Da LogP 0.05 TPSA 128.4	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@H]3NN=C(C(=O)c4cnccn4)[C@H]3…`
ZINC101363284 ZINC	0.656	346.3 Da LogP 0.05 TPSA 128.4	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@H]3NN=C(C(=O)c4cnccn4)[C@@H]…`
ZINC16037367 ZINC	0.656	346.3 Da LogP 0.05 TPSA 128.4	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@@H]3C(C(=O)c4cnccn4)=NN[C@H]…`
ZINC18124993 ZINC	0.656	346.3 Da LogP 0.05 TPSA 128.4	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@@H]3NN=C(C(=O)c4cnccn4)[C@@H…`
ZINC1857524240 ZINC	0.652	207.3 Da LogP -0.75 TPSA 60.0	✓ Ro5	✓ Clean	`COCCNCCOCCOCCO`
ZINC107287805 ZINC	0.635	438.4 Da LogP 2.95 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(C1=NN[C@H]2C(=O)N(c3ccccc3C(F)(F)F)C(=O)[C@…`
ZINC107287807 ZINC	0.635	438.4 Da LogP 2.95 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(C1=NN[C@@H]2C(=O)N(c3ccccc3C(F)(F)F)C(=O)[C…`
ZINC16034338 ZINC	0.635	438.4 Da LogP 2.95 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(C1=NN[C@H]2C(=O)N(c3ccccc3C(F)(F)F)C(=O)[C@…`
ZINC18153132 ZINC	0.635	438.4 Da LogP 2.95 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(C1=NN[C@@H]2C(=O)N(c3ccccc3C(F)(F)F)C(=O)[C…`
ZINC103462792 ZINC	0.633	322.3 Da LogP 0.75 TPSA 91.7	✓ Ro5	✓ Clean	`CCN1C(=O)[C@H]2NN=C(C(=O)c3ccc4ccccc4n3)[C@@H]2…`
ZINC103462794 ZINC	0.633	322.3 Da LogP 0.75 TPSA 91.7	✓ Ro5	✓ Clean	`CCN1C(=O)[C@H]2NN=C(C(=O)c3ccc4ccccc4n3)[C@H]2C…`
ZINC103462795 ZINC	0.633	322.3 Da LogP 0.75 TPSA 91.7	✓ Ro5	✓ Clean	`CCN1C(=O)[C@@H]2NN=C(C(=O)c3ccc4ccccc4n3)[C@@H]…`
ZINC5455887 ZINC	0.633	322.3 Da LogP 0.75 TPSA 91.7	✓ Ro5	✓ Clean	`CCN1C(=O)[C@@H]2C(C(=O)c3ccc4ccccc4n3)=NN[C@H]2…`
ZINC17835620 ZINC	0.625	400.4 Da LogP 1.94 TPSA 101.0	✓ Ro5	✓ Clean	`COc1ccccc1N1C(=O)[C@H]2NN=C(C(=O)c3ccc4ccccc4n3…`
ZINC100673359 ZINC	0.613	434.5 Da LogP 2.78 TPSA 102.6	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@H]3NN=C(C(=O)C(c4ccccc4)c4cc…`
ZINC103544561 ZINC	0.613	434.5 Da LogP 2.78 TPSA 102.6	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@@H]3C(C(=O)C(c4ccccc4)c4cccc…`
ZINC103544567 ZINC	0.613	434.5 Da LogP 2.78 TPSA 102.6	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@H]3NN=C(C(=O)C(c4ccccc4)c4cc…`
ZINC9411194 ZINC	0.613	434.5 Da LogP 2.78 TPSA 102.6	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@@H]3NN=C(C(=O)C(c4ccccc4)c4c…`
ZINC257355138 ZINC	0.600	479.9 Da LogP 0.65 TPSA 287.0	2 viol.	✓ Clean	`O=P(=O)O[P@](=O)(O)O[P@](=O)(O)O[P@@](=O)(O)O[P…`
ZINC5650743 ZINC	0.600	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC6403917 ZINC	0.600	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`

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.

Protein pemK

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

Main supporting evidence

Risks to review

Evidence gaps

Prioritization evidence

Off-target risk

Essentiality

Structure confidence

Binding-site evidence

Cross-references

Sequence

Chemistry

Sequence

Functional annotations

Subcellular localization

Enzyme Commission (EC)

Gene Ontology (GO)

Sequence domains and features

3D structure

Binding pockets · P2Rank

Binding pockets · P2Rank

Binding pockets · FPocket

Structural evidence

Ligand evidence