KpKP13 Protein target profile

MarR family transcriptional regulator

Accession: KP13_31616

Gene: AHE46531.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GR49

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Length 154

Pocket druggability (P2Rank · AlphaFold DB model) 0.055

Direct ligand evidence 0 52 total records

Functional annotation 0 EC 3 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. Strong predicted binding pocket FPocket selected-pocket score 0.78. This is a computational pocket signal, not binding validation. 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: 1.1% 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: 92.16 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) 0.055

Structure A0A0H3GR49

Pocket Pocket 1

Druggability (FPocket) 0.781

Structure A0A0H3GR49

Pocket Pocket 6

ColabFold model

P2Rank 0.115 · Pocket 1

FPocket 0.731 · Pocket 9

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 51 / 4744 genomes with a hit

Prevalence 1.1%

Sequence

Primary amino-acid sequence viewer.

MTEDELFARRPLGMRMAMVVRQWRAIIDSAITDTGLTQSSWTVLMQLHQLGDNVSVSELAEVQGIELPPLMRTLSLLEKQGYLVRSTSPYDKRIRLLTLTAEGRAILEKLSCVIETYQERVTQTIPEADLATFSATLNQIACRLRNIREEDNKI

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

17 records

Show feature table

Start	End	DB	Term	Name
29	130	SMART	SM00347	marrlong4
29	130	InterPro	IPR000835	MarR-type HTH domain
9	142	ProSiteProfiles	PS50995	MarR-type HTH domain profile.
9	142	InterPro	IPR000835	MarR-type HTH domain
71	86	PRINTS	PR00598	Bacterial regulatory protein MarR family signature
71	86	InterPro	IPR000835	MarR-type HTH domain
54	70	PRINTS	PR00598	Bacterial regulatory protein MarR family signature
54	70	InterPro	IPR000835	MarR-type HTH domain
90	106	PRINTS	PR00598	Bacterial regulatory protein MarR family signature
90	106	InterPro	IPR000835	MarR-type HTH domain
36	94	Pfam	PF01047	MarR family
36	94	InterPro	IPR000835	MarR-type HTH domain
9	151	Gene3D	G3DSA:1.10.10.10	-
9	151	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily
9	148	SUPERFAMILY	SSF46785	Winged helix DNA-binding domain
9	148	InterPro	IPR036390	Winged helix DNA-binding domain superfamily
14	150	PANTHER	PTHR42756	TRANSCRIPTIONAL REGULATOR, MARR

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

0.055

Show in viewer

Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #6

0.781

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_A0A0H3GR49	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_31616	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 2 records from similar proteins

Structural ligands 2 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

SAL PDB via homolog 138.1 Da · LogP 1.09 · TPSA 57.5 Open detail RCSB PDB

WCA PDB via homolog Detail RCSB PDB

ZINC400143 ZINC proposed compound · Tanimoto 0.652 Detail ZINC

ZINC38392758 ZINC proposed compound · Tanimoto 0.650 Detail ZINC

ZINC404363 ZINC proposed compound · Tanimoto 0.650 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
SAL RCSB PDB	3BPX	O26413	138.1 Da LogP 1.09 TPSA 57.5	✓ Ro5	✓ Clean	`c1ccc(c(c1)C(=O)O)O`
WCA RCSB PDB	5CYV	Q0S6D0	913.7 Da LogP 0.08 TPSA 383.9	3 viol.	✓ Clean	`CC(C)(COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([…`

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
ZINC400143 ZINC	0.652	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1-c1ccccc1O`
ZINC38392758 ZINC	0.650	242.2 Da LogP 2.16 TPSA 74.6	✓ Ro5	Alert	`O=C(C(=O)c1ccccc1O)c1ccccc1O`
ZINC404363 ZINC	0.650	214.2 Da LogP 2.33 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(c1ccccc1O)c1ccccc1O`
ZINC105146 ZINC	0.619	242.2 Da LogP 2.75 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1-c1ccccc1C(=O)O`
ZINC2062 ZINC	0.593	258.2 Da LogP 2.31 TPSA 83.8	✓ Ro5	✓ Clean	`O=C(Oc1ccccc1C(=O)O)c1ccccc1O`
ZINC82369423 ZINC	0.583	217.0 Da LogP 1.85 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cccc(O)c1Br`
ZINC95713705 ZINC	0.583	264.0 Da LogP 1.70 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cccc(O)c1I`
ZINC149361708 ZINC	0.577	230.2 Da LogP 2.46 TPSA 77.8	✓ Ro5	✓ Clean	`O=C(O)c1cccc(-c2ccccc2O)c1O`
ZINC1577073 ZINC	0.577	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cc(-c2ccccc2)ccc1O`
ZINC39194529 ZINC	0.577	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccccc2)cc1O`
ZINC148036793 ZINC	0.571	378.3 Da LogP 3.53 TPSA 110.1	✓ Ro5	✓ Clean	`O=C(Oc1ccccc1C(=O)Oc1ccccc1C(=O)O)c1ccccc1O`
ZINC1600331 ZINC	0.571	330.2 Da LogP 2.15 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)O)c1-c1c(C(=O)O)cccc1C(=O)O`
ZINC1670022 ZINC	0.571	258.2 Da LogP 2.03 TPSA 94.8	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)c1cc(O)ccc1O`
ZINC164706 ZINC	0.565	201.0 Da LogP 2.15 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1Br`
ZINC2453187 ZINC	0.565	257.2 Da LogP 1.67 TPSA 86.6	✓ Ro5	✓ Clean	`O=C(NC(=O)c1ccccc1O)c1ccccc1O`
ZINC90931 ZINC	0.565	248.0 Da LogP 1.99 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1I`
ZINC553173 ZINC	0.560	326.4 Da LogP 1.70 TPSA 81.1	✓ Ro5	✓ Clean	`O=C(c1ccccc1O)N1CCN(C(=O)c2ccccc2O)CC1`
ZINC1616707 ZINC	0.552	270.3 Da LogP 2.91 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(CCc1ccccc1C(=O)O)c1ccccc1O`
ZINC388710 ZINC	0.545	210.1 Da LogP 0.78 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)O)c1C(=O)O`
ZINC389564 ZINC	0.545	216.2 Da LogP 2.24 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)O)c2ccccc12`
ZINC4289585 ZINC	0.545	226.1 Da LogP 0.49 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(=O)O)c(C(=O)O)cc1O`
ZINC45070868 ZINC	0.545	216.2 Da LogP 2.24 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1cccc2c(C(=O)O)cccc12`
ZINC146669761 ZINC	0.542	274.2 Da LogP 2.16 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)c(O)c2)cc1O`
ZINC154566 ZINC	0.542	257.2 Da LogP 2.83 TPSA 86.6	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1Nc1ccccc1C(=O)O`
ZINC157193 ZINC	0.542	226.2 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)c1ccccc1`
ZINC1604722 ZINC	0.542	326.3 Da LogP 2.93 TPSA 108.7	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)CCC(=O)c1ccccc1C(=O)O`
ZINC256346309 ZINC	0.542	270.2 Da LogP 3.50 TPSA 99.3	✓ Ro5	Alert	`O=C(O)c1ccccc1N=Nc1ccccc1C(=O)O`
ZINC34572642 ZINC	0.542	274.2 Da LogP 2.16 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)c1cc(-c2ccc(O)c(C(=O)O)c2)ccc1O`
ZINC3845505 ZINC	0.542	268.3 Da LogP 3.25 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1/C=C/c1ccccc1C(=O)O`
ZINC410108 ZINC	0.542	258.2 Da LogP 2.88 TPSA 83.8	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1Oc1ccccc1C(=O)O`
ZINC5369059 ZINC	0.542	274.3 Da LogP 3.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1Sc1ccccc1C(=O)O`
ZINC5771961 ZINC	0.542	256.3 Da LogP 2.67 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1Cc1ccccc1C(=O)O`
ZINC62723773 ZINC	0.542	270.2 Da LogP 3.50 TPSA 99.3	✓ Ro5	Alert	`O=C(O)c1ccccc1/N=N/c1ccccc1C(=O)O`
ZINC17991503 ZINC	0.538	240.3 Da LogP 2.85 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(CC(=O)c1ccccc1O)c1ccccc1`
ZINC1845893 ZINC	0.538	201.2 Da LogP 0.03 TPSA 97.5	✓ Ro5	✓ Clean	`NS(=O)(=O)c1ccccc1C(=O)O`
ZINC2057 ZINC	0.538	213.2 Da LogP 2.64 TPSA 49.3	✓ Ro5	✓ Clean	`O=C(Nc1ccccc1)c1ccccc1O`
ZINC2559138 ZINC	0.538	212.2 Da LogP 2.82 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(Cc1ccccc1)c1ccccc1O`
ZINC38545 ZINC	0.538	214.2 Da LogP 2.61 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(Oc1ccccc1)c1ccccc1O`
ZINC3157157 ZINC	0.533	276.7 Da LogP 2.97 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)c1cc(Cl)ccc1O`
ZINC393330 ZINC	0.533	256.3 Da LogP 2.63 TPSA 74.6	✓ Ro5	✓ Clean	`Cc1ccc(O)c(C(=O)c2ccccc2C(=O)O)c1`
ZINC391925 ZINC	0.526	254.1 Da LogP 0.48 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(=O)O)c(C(=O)O)cc1C(=O)O`
ZINC1559267 ZINC	0.522	292.0 Da LogP 1.69 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)O)c1I`
ZINC3158512 ZINC	0.522	245.0 Da LogP 1.85 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)O)c1Br`
ZINC391804 ZINC	0.522	216.2 Da LogP 2.24 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1cc2ccccc2cc1C(=O)O`
ZINC6750304 ZINC	0.522	200.6 Da LogP 1.74 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)O)c1Cl`
ZINC173169 ZINC	0.520	306.3 Da LogP 1.92 TPSA 108.7	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1S(=O)(=O)c1ccccc1C(=O)O`
ZINC2048532660 ZINC	0.520	350.3 Da LogP 3.83 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccc(C(=O)O)c(O)c3)cc2)cc1O`
ZINC2048532872 ZINC	0.520	350.3 Da LogP 3.83 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)c1cc(-c2ccc(-c3ccc(O)c(C(=O)O)c3)cc2)ccc1O`
ZINC253497329 ZINC	0.520	266.0 Da LogP 1.34 TPSA 54.4	✓ Ro5	✓ Clean	`O=[IH2]c1ccccc1C(=O)O`
ZINC4247392 ZINC	0.520	348.4 Da LogP 4.57 TPSA 98.7	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1Nc1ccccc1Nc1ccccc1C(=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 A0A0H3GR49