KpATCC43816 Protein target profile

lacI transcriptional repressor

Accession: VK055_2116

Gene: lacI2 AIK80721.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GNN4

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Length 356

Pocket druggability (P2Rank · AlphaFold DB model) 0.923

Direct ligand evidence 0 28 total records

Functional annotation 0 EC 4 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. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.92. Structure available AlphaFold DB model + ColabFold model 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: No hit
Gut microbiome similarity: 0.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 42.776 Higher values support similarity to known essential genes.
DEG E-value: 4.2e-91 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 91.58 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) 0.923

Structure A0A0H3GNN4

Pocket Pocket 1

Druggability (FPocket) 0.889

Structure A0A0H3GNN4

Pocket Pocket 1

ColabFold model

P2Rank 0.915 · Pocket 1

FPocket 0.451 · Pocket 3

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 29 / 4744 genomes with a hit

Prevalence 0.6%

Metabolic context

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

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MKSKSATLEDVARHAGVSYQTVSRVLNKSANVSEATRRKVEKSIEALRYVPNRLAQQLVGKESQTVGLVTISLAWHAPSQVAAAVKRYANLEGYQVLISMIDESVNQSIQDSINELKSQRVDKVIINVPLETEQAQKIAADNDDIVCLFLDVDPYSSVFNVSFNPADGTRASVKYLYEMGHREIALLAGPDSSVSAKLRLKSWLETLDGYGLKPVTVLHGNWDAQSGYAGALQMLRETPNFSAVLVGNDQMALGVLSAFHQHQVAVPGEKSVIGYDDTYESSFFYPALSTVSLDLDLQGKEAVRRILASTSGAPHTSSILPARLVIRHSSGARIEQGKDLQAIAEQLRAIAHRLAP

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
GO:0000976 Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

25 records

Show feature table

Start	End	DB	Term	Name
63	327	SUPERFAMILY	SSF53822	Periplasmic binding protein-like I
63	327	InterPro	IPR028082	Periplasmic binding protein-like I
10	60	CDD	cd01392	HTH_LacI
10	60	InterPro	IPR000843	LacI-type HTH domain
1	335	PANTHER	PTHR30146	LACI-RELATED TRANSCRIPTIONAL REPRESSOR
8	26	ProSitePatterns	PS00356	LacI-type HTH domain signature.
173	330	Pfam	PF13377	Periplasmic binding protein-like domain
173	330	InterPro	IPR046335	Transcriptional regulator LacI/GalR-like, sensor domain
164	325	Gene3D	G3DSA:3.40.50.2300	-
5	75	SMART	SM00354	laci3
5	75	InterPro	IPR000843	LacI-type HTH domain
65	329	CDD	cd01574	PBP1_LacI
82	321	Gene3D	G3DSA:3.40.50.2300	-
6	60	ProSiteProfiles	PS50932	LacI-type HTH domain profile.
6	60	InterPro	IPR000843	LacI-type HTH domain
5	63	SUPERFAMILY	SSF47413	lambda repressor-like DNA-binding domains
5	63	InterPro	IPR010982	Lambda repressor-like, DNA-binding domain superfamily
3	62	Gene3D	G3DSA:1.10.260.40	-
3	62	InterPro	IPR010982	Lambda repressor-like, DNA-binding domain superfamily
17	27	PRINTS	PR00036	LacI bacterial regulatory protein HTH signature
17	27	InterPro	IPR000843	LacI-type HTH domain
7	17	PRINTS	PR00036	LacI bacterial regulatory protein HTH signature
7	17	InterPro	IPR000843	LacI-type HTH domain
7	52	Pfam	PF00356	Bacterial regulatory proteins, lacI family
7	52	InterPro	IPR000843	LacI-type HTH domain

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

0.923

Likely same site as FPocket 1 3.3 Å 21 shared residues 84% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.161

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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

0.889 Unusual size

Likely same site as P2Rank 1 3.3 Å 21 shared residues 84% 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_A0A0H3GNN4	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_2116	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.

28 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 5 records from similar proteins

Structural ligands 5 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 23 similarity-based ZINC candidates

Best available ligand signal

171 PDB via homolog 201.2 Da · LogP 0.99 · TPSA 66.4 Open detail RCSB PDB

6MP PDB via homolog Detail RCSB PDB

ADE PDB via homolog Detail RCSB PDB

GUN PDB via homolog Detail RCSB PDB

HPA 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
171 RCSB PDB	1SXG	P46828	201.2 Da LogP 0.99 TPSA 66.4	✓ Ro5	✓ Clean	`c1ccc(cc1)NCCS(=O)(=O)O`
6MP RCSB PDB	2PUA	P0ACP7	134.1 Da LogP 0.66 TPSA 54.5	✓ Ro5	✓ Clean	`Cc1c2c(nc[nH]2)ncn1`
ADE RCSB PDB	2PUB	P0ACP7	135.1 Da LogP -0.06 TPSA 80.5	✓ Ro5	✓ Clean	`c1[nH]c2c(n1)c(ncn2)N`
GUN RCSB PDB	1WET	P0ACP7	151.1 Da LogP -0.77 TPSA 100.5	✓ Ro5	✓ Clean	`c1[nH]c2c(n1)C(=O)NC(=N2)N`
HPA RCSB PDB	1BDH	P0ACP7	136.1 Da LogP -0.35 TPSA 74.4	✓ Ro5	✓ Clean	`c1[nH]c2c(n1)N=CNC2=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
ZINC2170599 ZINC	1.000	201.2 Da LogP 0.99 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNc1ccccc1`
ZINC2170604 ZINC	0.786	215.3 Da LogP 1.38 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNc1ccccc1`
ZINC9974955 ZINC	0.625	215.0 Da LogP 0.41 TPSA 74.4	✓ Ro5	✓ Clean	`O=c1[nH]c(Br)nc2[nH]cnc12`
ZINC4430249 ZINC	0.571	246.0 Da LogP 0.96 TPSA 54.5	✓ Ro5	✓ Clean	`Ic1ncnc2nc[nH]c12`
ZINC8627299 ZINC	0.571	262.0 Da LogP 0.25 TPSA 74.4	✓ Ro5	✓ Clean	`O=c1[nH]cnc2nc(I)[nH]c12`
ZINC1648199 ZINC	0.560	212.3 Da LogP 3.21 TPSA 24.1	✓ Ro5	✓ Clean	`c1ccc(NCCNc2ccccc2)cc1`
ZINC8615502 ZINC	0.552	270.3 Da LogP 1.17 TPSA 108.9	✓ Ro5	✓ Clean	`c1nc(Sc2ncnc3nc[nH]c23)c2[nH]cnc2n1`
ZINC12174637 ZINC	0.545	229.3 Da LogP 0.90 TPSA 83.5	✓ Ro5	✓ Clean	`O=C(CCS(=O)(=O)O)Nc1ccccc1`
ZINC43463386 ZINC	0.533	261.0 Da LogP 0.54 TPSA 80.5	✓ Ro5	✓ Clean	`Nc1nc(I)nc2[nH]cnc12`
ZINC4552271 ZINC	0.533	237.5 Da LogP 2.18 TPSA 54.5	✓ Ro5	✓ Clean	`ClC(Cl)(Cl)c1ncnc2[nH]cnc12`
ZINC4707072 ZINC	0.533	214.0 Da LogP 0.70 TPSA 80.5	✓ Ro5	✓ Clean	`Nc1nc(Br)nc2[nH]cnc12`
ZINC12428236 ZINC	0.529	232.2 Da LogP -0.74 TPSA 146.4	✓ Ro5	✓ Clean	`Nc1c2nc[nH]c2c(N)c2[nH]c(=O)c(=O)[nH]c12`
ZINC4806366 ZINC	0.529	231.3 Da LogP 0.35 TPSA 86.6	✓ Ro5	✓ Clean	`O=S(=O)(O)C[C@@H](O)CNc1ccccc1`
ZINC1847900 ZINC	0.519	226.3 Da LogP 3.60 TPSA 24.1	✓ Ro5	✓ Clean	`c1ccc(NCCCNc2ccccc2)cc1`
ZINC1574855 ZINC	0.516	204.1 Da LogP 0.67 TPSA 74.4	✓ Ro5	✓ Clean	`O=c1[nH]cnc2nc(C(F)(F)F)[nH]c12`
ZINC95415357 ZINC	0.515	228.3 Da LogP 1.04 TPSA 58.2	✓ Ro5	✓ Clean	`CCS(=O)(=O)NCCNc1ccccc1`
ZINC148572871 ZINC	0.500	263.3 Da LogP 2.55 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)c1ccccc1CNc1ccccc1`
ZINC1511379 ZINC	0.500	230.0 Da LogP -0.01 TPSA 100.4	✓ Ro5	✓ Clean	`Nc1nc2[nH]c(Br)nc2c(=O)[nH]1`
ZINC238628781 ZINC	0.500	213.2 Da LogP 0.71 TPSA 87.3	✓ Ro5	✓ Clean	`O=c1[nH]c(-c2ccccn2)nc2[nH]cnc12`
ZINC4878369 ZINC	0.500	277.0 Da LogP -0.17 TPSA 100.4	✓ Ro5	✓ Clean	`Nc1nc2[nH]c(I)nc2c(=O)[nH]1`
ZINC5543260 ZINC	0.500	200.2 Da LogP -0.40 TPSA 108.8	✓ Ro5	✓ Clean	`O=S(=O)(O)c1ncnc2[nH]cnc12`
ZINC6514392 ZINC	0.500	260.3 Da LogP 1.65 TPSA 90.3	✓ Ro5	✓ Clean	`N=C(Nc1ccccc1)SCCS(=O)(=O)O`
ZINC757131928 ZINC	0.500	227.2 Da LogP 0.25 TPSA 103.1	✓ Ro5	✓ Clean	`N#Cc1ccc(NCCS(=O)(=O)O)cn1`

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 A0A0H3GNN4