KpKP13 Protein target profile

putative HTH-type transcriptional regulator ltrA

Accession: KP13_04642

Gene: AHE44098.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GUV7

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Length 303

Pocket druggability (P2Rank · AlphaFold DB model) 0.888

Direct ligand evidence 0 52 total records

Functional annotation 0 EC 4 GO

Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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

Main supporting evidence

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.89, FPocket 0.75). Use the 3D pocket comparison to verify whether they identify the same site. 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. Strong predicted binding pocket FPocket selected-pocket score 0.75. This is a computational pocket signal, not binding validation. 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: 0.3% 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: 90.67 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) 0.888

Structure A0A0H3GUV7

Pocket Pocket 1

Druggability (FPocket) 0.753

Structure A0A0H3GUV7

Pocket Pocket 22

ColabFold model

P2Rank 0.808 · Pocket 1

FPocket 0.953 · Pocket 2

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 14 / 4744 genomes with a hit

Prevalence 0.3%

Sequence

Primary amino-acid sequence viewer.

MNTSIPWEWYRTFLAVLQEGSLSGASRTLNITQPTAGRHIAGLEAALGQALFTRSQTGLLATDAALALRMHAEAMDNTARALERTAANFSRDRAELRGVVRVAASEVVGAEVLPPLVARLRQACPNIVIELMLSNRFQDLLHREADIAVRMVAPQQEQLIARRLGRIELGLHATAAYLTRQGLPTTLDDLASHALIGFDSTTPLVRRALQAYPRFQREAFAMRTDSDLAQLSLIRAGAGIGICQAPLADGIIPLQRVLAADFSLYLDTWLVMHEDLRHSPACKRVFDFLAQGLQAYIRGPLAS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

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:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
GO:0006351 The synthesis of an RNA transcript from a DNA template.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
5	118	SUPERFAMILY	SSF46785	Winged helix DNA-binding domain
5	118	InterPro	IPR036390	Winged helix DNA-binding domain superfamily
94	293	Pfam	PF03466	LysR substrate binding domain
94	293	InterPro	IPR005119	LysR, substrate-binding
2	88	Gene3D	G3DSA:1.10.10.10	-
2	88	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily
93	292	Gene3D	G3DSA:3.40.190.290	-
33	43	PRINTS	PR00039	LysR bacterial regulatory protein HTH signature
33	43	InterPro	IPR000847	Transcription regulator HTH, LysR
43	54	PRINTS	PR00039	LysR bacterial regulatory protein HTH signature
43	54	InterPro	IPR000847	Transcription regulator HTH, LysR
22	33	PRINTS	PR00039	LysR bacterial regulatory protein HTH signature
22	33	InterPro	IPR000847	Transcription regulator HTH, LysR
5	62	ProSiteProfiles	PS50931	LysR-type HTH domain profile.
5	62	InterPro	IPR000847	Transcription regulator HTH, LysR
95	296	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
6	293	PANTHER	PTHR30126	HTH-TYPE TRANSCRIPTIONAL REGULATOR
8	65	Pfam	PF00126	Bacterial regulatory helix-turn-helix protein, lysR family
8	65	InterPro	IPR000847	Transcription regulator HTH, LysR

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

0.888

Likely same site as FPocket 22 0.4 Å 26 shared residues 96% 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 #22

0.753 Unusual size

Likely same site as P2Rank 1 0.4 Å 26 shared residues 96% of smaller site

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Surrounding area

Pocket 2 FPocket #3

0.421

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Surrounding area

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.808

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Surrounding area

Pocket 2 P2Rank #2

0.008

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Surrounding area

Pocket 3 P2Rank #3

0.004

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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_A0A0H3GUV7	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_04642	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.

52 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 4 records from similar proteins

Structural ligands 4 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 48 similarity-based ZINC candidates

Best available ligand signal

CCU PDB via homolog 142.1 Da · LogP 0.27 · TPSA 74.6 Open detail RCSB PDB

FLC PDB via homolog Detail RCSB PDB

PCI PDB via homolog Detail RCSB PDB

T6C PDB via homolog Detail RCSB PDB

ZINC1529471 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
CCU RCSB PDB	3GLB	P07774	142.1 Da LogP 0.27 TPSA 74.6	✓ Ro5	✓ Clean	`C(=C/C(=O)O)/C=C\C(=O)O`
FLC RCSB PDB	5ZZO	A0A0D1IHL7	189.1 Da LogP -5.25 TPSA 140.6	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O`
PCI RCSB PDB	4RPN	P52679	266.3 Da LogP 4.66 TPSA 20.2	✓ Ro5	✓ Clean	`c1(c(c(c(c(c1Cl)Cl)Cl)Cl)Cl)O`
T6C RCSB PDB	4RPO	P52679	197.4 Da LogP 3.35 TPSA 20.2	✓ Ro5	✓ Clean	`c1c(cc(c(c1Cl)O)Cl)Cl`

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
ZINC1529471 ZINC	1.000	266.3 Da LogP 4.66 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1c(Cl)c(Cl)c(Cl)c(Cl)c1Cl`
ZINC225408 ZINC	0.900	247.9 Da LogP 3.71 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1c(Cl)c(Cl)c(O)c(Cl)c1Cl`
ZINC154748 ZINC	0.818	247.9 Da LogP 3.71 TPSA 40.5	✓ Ro5	Alert	`Oc1c(O)c(Cl)c(Cl)c(Cl)c1Cl`
ZINC1657278 ZINC	0.684	241.9 Da LogP 3.46 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1c(Cl)cc(Cl)cc1Br`
ZINC394287 ZINC	0.650	288.9 Da LogP 3.30 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1c(Cl)cc(Cl)cc1I`
ZINC1621105 ZINC	0.579	241.9 Da LogP 3.46 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1c(Cl)cc(Br)cc1Cl`
ZINC3165572 ZINC	0.579	288.9 Da LogP 3.30 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1c(Cl)cc(I)cc1Cl`
ZINC1214789 ZINC	0.565	388.1 Da LogP 4.54 TPSA 74.6	✓ Ro5	✓ Clean	`O=S(=O)(c1cc(Cl)cc(Cl)c1O)c1cc(Cl)cc(Cl)c1O`
ZINC140063217 ZINC	0.565	206.1 Da LogP 2.77 TPSA 23.5	✓ Ro5	✓ Clean	`CN(C)c1cc(Cl)cc(Cl)c1O`
ZINC39208718 ZINC	0.565	219.1 Da LogP 4.00 TPSA 20.2	✓ Ro5	✓ Clean	`CC(C)(C)c1cc(Cl)cc(Cl)c1O`
ZINC409156 ZINC	0.565	207.0 Da LogP 2.40 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cc(Cl)cc(Cl)c1O`
ZINC608214 ZINC	0.565	372.1 Da LogP 4.88 TPSA 57.5	✓ Ro5	✓ Clean	`O=S(c1cc(Cl)cc(Cl)c1O)c1cc(Cl)cc(Cl)c1O`
ZINC98180109 ZINC	0.563	246.9 Da LogP 3.59 TPSA 46.2	✓ Ro5	✓ Clean	`Nc1c(O)c(Cl)c(Cl)c(Cl)c1Cl`
ZINC157940 ZINC	0.556	213.4 Da LogP 3.06 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1c(Cl)cc(Cl)c(O)c1Cl`
ZINC100303564 ZINC	0.542	206.0 Da LogP 2.51 TPSA 52.8	✓ Ro5	✓ Clean	`O/N=C\c1cc(Cl)cc(Cl)c1O`
ZINC12433162 ZINC	0.542	227.1 Da LogP 2.28 TPSA 57.5	✓ Ro5	✓ Clean	`O=[S@](O)c1cc(Cl)cc(Cl)c1O`
ZINC1555814 ZINC	0.542	243.1 Da LogP 1.95 TPSA 74.6	✓ Ro5	✓ Clean	`O=S(=O)(O)c1cc(Cl)cc(Cl)c1O`
ZINC156199 ZINC	0.542	205.0 Da LogP 2.90 TPSA 37.3	✓ Ro5	✓ Clean	`CC(=O)c1cc(Cl)cc(Cl)c1O`
ZINC16892077 ZINC	0.542	206.0 Da LogP 2.51 TPSA 52.8	✓ Ro5	✓ Clean	`O/N=C/c1cc(Cl)cc(Cl)c1O`
ZINC37594061 ZINC	0.542	206.0 Da LogP 1.80 TPSA 63.3	✓ Ro5	✓ Clean	`NC(=O)c1cc(Cl)cc(Cl)c1O`
ZINC71462836 ZINC	0.542	221.0 Da LogP 2.33 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)Cc1cc(Cl)cc(Cl)c1O`
ZINC1719222 ZINC	0.529	215.9 Da LogP 4.30 TPSA 0.0	✓ Ro5	✓ Clean	`Clc1cc(Cl)c(Cl)c(Cl)c1`
ZINC1600062 ZINC	0.524	219.1 Da LogP 4.00 TPSA 20.2	✓ Ro5	✓ Clean	`CC(C)(C)c1cc(Cl)c(O)c(Cl)c1`
ZINC12405073 ZINC	0.520	208.0 Da LogP 2.61 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1cc(Cl)cc(Cl)c1O`
ZINC1635785 ZINC	0.520	242.1 Da LogP 1.35 TPSA 80.4	✓ Ro5	Alert	`NS(=O)(=O)c1cc(Cl)cc(Cl)c1O`
ZINC1641216 ZINC	0.520	239.1 Da LogP 4.37 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1c(Cl)cc(Cl)cc1-c1ccccc1`
ZINC254869162 ZINC	0.520	205.0 Da LogP 1.99 TPSA 58.6	✓ Ro5	Alert	`NN=Cc1cc(Cl)cc(Cl)c1O`
ZINC263623444 ZINC	0.520	229.0 Da LogP 3.30 TPSA 29.5	✓ Ro5	✓ Clean	`Oc1c(Cl)cc(Cl)cc1OC(F)F`
ZINC95917762 ZINC	0.520	205.0 Da LogP 1.99 TPSA 58.6	✓ Ro5	Alert	`N/N=C\c1cc(Cl)cc(Cl)c1O`
ZINC1100714 ZINC	0.500	388.1 Da LogP 4.54 TPSA 74.6	✓ Ro5	✓ Clean	`O=S(=O)(c1cc(Cl)c(O)c(Cl)c1)c1cc(Cl)c(O)c(Cl)c1`
ZINC138298292 ZINC	0.500	241.9 Da LogP 3.46 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1cc(Cl)cc(Cl)c1Br`
ZINC141007693 ZINC	0.500	229.0 Da LogP 3.30 TPSA 29.5	✓ Ro5	✓ Clean	`Oc1c(Cl)cc(OC(F)F)cc1Cl`
ZINC1504178 ZINC	0.500	231.9 Da LogP 4.01 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1c(Cl)c(Cl)cc(Cl)c1Cl`
ZINC156492 ZINC	0.500	207.0 Da LogP 2.40 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cc(Cl)c(O)c(Cl)c1`
ZINC1636564 ZINC	0.500	220.1 Da LogP 2.66 TPSA 49.3	✓ Ro5	✓ Clean	`CC(=O)Nc1cc(Cl)cc(Cl)c1O`
ZINC1846640 ZINC	0.500	261.9 Da LogP 4.01 TPSA 29.5	✓ Ro5	✓ Clean	`COc1c(Cl)c(Cl)c(O)c(Cl)c1Cl`
ZINC22143662 ZINC	0.500	206.1 Da LogP 2.42 TPSA 32.3	✓ Ro5	Alert	`CNCc1cc(Cl)cc(Cl)c1O`
ZINC226281263 ZINC	0.500	230.1 Da LogP 2.28 TPSA 50.9	✓ Ro5	✓ Clean	`Oc1c(Cl)cc(Cl)cc1-n1cnnc1`
ZINC28278356 ZINC	0.500	380.4 Da LogP 3.25 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1c(I)cc(Cl)cc1I`
ZINC31614398 ZINC	0.500	220.1 Da LogP 2.76 TPSA 23.5	✓ Ro5	Alert	`CN(C)Cc1cc(Cl)cc(Cl)c1O`
ZINC32914678 ZINC	0.500	288.9 Da LogP 3.30 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1cc(Cl)cc(Cl)c1I`
ZINC3899447 ZINC	0.500	232.9 Da LogP 3.40 TPSA 33.1	✓ Ro5	✓ Clean	`Oc1c(Cl)c(Cl)nc(Cl)c1Cl`
ZINC390985 ZINC	0.500	307.3 Da LogP 4.25 TPSA 0.0	✓ Ro5	✓ Clean	`Clc1cc(Cl)c(I)c(Cl)c1`
ZINC393669 ZINC	0.500	225.5 Da LogP 3.97 TPSA 20.2	✓ Ro5	✓ Clean	`Cc1c(Cl)c(C)c(Cl)c(O)c1Cl`
ZINC394419 ZINC	0.500	231.9 Da LogP 4.01 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1c(Cl)cc(Cl)c(Cl)c1Cl`
ZINC395144 ZINC	0.500	206.1 Da LogP 2.77 TPSA 23.5	✓ Ro5	✓ Clean	`CN(C)c1cc(Cl)c(O)c(Cl)c1`
ZINC397592 ZINC	0.500	286.4 Da LogP 3.57 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1c(Br)cc(Cl)cc1Br`
ZINC4141920 ZINC	0.500	329.0 Da LogP 4.01 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1c(Cl)cc(Cl)cc1C(O)(C(F)(F)F)C(F)(F)F`

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 A0A0H3GUV7