Protein target profile

VK055_1021

bacterial regulatory, gntR family protein

Genome: KpATCC43816 Gene: AIK79644.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GS62

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Length 143

Pocket druggability 0.984

Direct ligand evidence 0 62 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 0.98. 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: 0.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 30.702 Higher values support similarity to known essential genes.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 92.99 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.984

Structure A0A0H3GS62

Pocket Pocket 5

P2Rank 0.146

Structure A0A0H3GS62

Pocket Pocket 1

ColabFold model

FPocket 0.904 · Pocket 1

P2Rank 0.223 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 27 / 4744 genomes with a hit

Prevalence 0.6%

Cross-references

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

Sequence

UniProt A0A0H3GS62

Sequence

Primary amino-acid sequence viewer.

MDNRQLTFSHLLYLTAHHWRLAVNRRLKNLGLSQASWVAVASIARHQQPLSQSELAQELGVESPTIVPLIHRLVALGLVERVTTASDKRKRLLVVTDKGKALYEQVKTVADDLREEILTAITPQEQEQTQRVLEKLLREVEKK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

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:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
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.

19 records

Show feature table

Start	End	DB	Term	Name
6	143	Gene3D	G3DSA:1.10.10.10	-
6	143	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily
30	89	Pfam	PF12802	MarR family
30	89	InterPro	IPR000835	MarR-type HTH domain
5	140	SUPERFAMILY	SSF46785	Winged helix DNA-binding domain
5	140	InterPro	IPR036390	Winged helix DNA-binding domain superfamily
25	126	SMART	SM00347	marrlong4
25	126	InterPro	IPR000835	MarR-type HTH domain
50	66	PRINTS	PR00598	Bacterial regulatory protein MarR family signature
50	66	InterPro	IPR000835	MarR-type HTH domain
116	136	PRINTS	PR00598	Bacterial regulatory protein MarR family signature
116	136	InterPro	IPR000835	MarR-type HTH domain
67	82	PRINTS	PR00598	Bacterial regulatory protein MarR family signature
67	82	InterPro	IPR000835	MarR-type HTH domain
86	102	PRINTS	PR00598	Bacterial regulatory protein MarR family signature
86	102	InterPro	IPR000835	MarR-type HTH domain
5	138	ProSiteProfiles	PS50995	MarR-type HTH domain profile.
5	138	InterPro	IPR000835	MarR-type HTH domain
3	143	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 · FPocket

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

Site 1 FPocket #5

0.984

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Surrounding area

Site 2 FPocket #1

0.262

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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1

0.146

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Surrounding area

Binding pockets · FPocket

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

Site 1 FPocket #1

0.904

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Surrounding area

Site 2 FPocket #10

0.413

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Surrounding area

Site 3 FPocket #2

0.232

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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_A0A0H3GS62	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_1021	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.

62 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 12 records from similar proteins

Structural ligands 12 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

3IB PDB via homolog 203.2 Da · LogP 2.58 · TPSA 53.1 Open detail RCSB PDB

BEZ PDB via homolog Detail RCSB PDB

CAQ PDB via homolog Detail RCSB PDB

CFA PDB via homolog Detail RCSB PDB

ET 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
3IB RCSB PDB	7KIG	C5CSP2	203.2 Da LogP 2.58 TPSA 53.1	✓ Ro5	✓ Clean	`c1ccc2c(c1)c(c[nH]2)CCCC(=O)O`
BEZ RCSB PDB	7KFS	C5CSP2	122.1 Da LogP 1.38 TPSA 37.3	✓ Ro5	✓ Clean	`c1ccc(cc1)C(=O)O`
CAQ RCSB PDB	7KK0	C5CSP2	110.1 Da LogP 1.10 TPSA 40.5	✓ Ro5	Alert	`c1ccc(c(c1)O)O`
CFA RCSB PDB	7KKI	C5CSP2	221.0 Da LogP 2.46 TPSA 46.5	✓ Ro5	✓ Clean	`c1cc(c(cc1Cl)Cl)OCC(=O)O`
ET RCSB PDB	5FFZ	Q5Y812	314.4 Da LogP 4.13 TPSA 55.9	✓ Ro5	Alert	`CC[n+]1c2cc(ccc2c3ccc(cc3c1c4ccccc4)N)N`
HID RCSB PDB	7KKC	C5CSP2	191.2 Da LogP 1.50 TPSA 73.3	✓ Ro5	✓ Clean	`c1cc2c(cc1O)c(c[nH]2)CC(=O)O`
IAC RCSB PDB	7KFO	C5CSP2	175.2 Da LogP 1.79 TPSA 53.1	✓ Ro5	✓ Clean	`c1ccc2c(c1)c(c[nH]2)CC(=O)O`
ICO RCSB PDB	7KFQ	C5CSP2	161.2 Da LogP 1.87 TPSA 53.1	✓ Ro5	✓ Clean	`c1ccc2c(c1)c(c[nH]2)C(=O)O`
IOP RCSB PDB	7KH3	C5CSP2	189.2 Da LogP 2.19 TPSA 53.1	✓ Ro5	✓ Clean	`c1ccc2c(c1)c(c[nH]2)CCC(=O)O`
SAL RCSB PDB	7KJL	C5CSP2	138.1 Da LogP 1.09 TPSA 57.5	✓ Ro5	✓ Clean	`c1ccc(c(c1)C(=O)O)O`
WCA RCSB PDB	6C28	Q6N8V9	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]([…`
WOM RCSB PDB	7KJQ	C5CSP2	241.5 Da LogP 2.32 TPSA 76.2	✓ Ro5	✓ Clean	`c1(c(c(nc(c1Cl)Cl)C(=O)O)Cl)N`

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
ZINC119632 ZINC	1.000	314.4 Da LogP 4.13 TPSA 55.9	✓ Ro5	Alert	`CC[n+]1c(-c2ccccc2)c2cc(N)ccc2c2ccc(N)cc21`
ZINC1237662 ZINC	1.000	241.5 Da LogP 2.32 TPSA 76.2	✓ Ro5	✓ Clean	`Nc1c(Cl)c(Cl)nc(C(=O)O)c1Cl`
ZINC57143 ZINC	1.000	221.0 Da LogP 2.46 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)COc1ccc(Cl)cc1Cl`
ZINC57378 ZINC	1.000	203.2 Da LogP 2.58 TPSA 53.1	✓ Ro5	✓ Clean	`O=C(O)CCCc1c[nH]c2ccccc12`
ZINC2566960 ZINC	0.909	231.3 Da LogP 3.36 TPSA 53.1	✓ Ro5	✓ Clean	`O=C(O)CCCCCc1c[nH]c2ccccc12`
ZINC37632578 ZINC	0.909	217.3 Da LogP 2.97 TPSA 53.1	✓ Ro5	✓ Clean	`O=C(O)CCCCc1c[nH]c2ccccc12`
ZINC37632580 ZINC	0.909	245.3 Da LogP 3.75 TPSA 53.1	✓ Ro5	✓ Clean	`O=C(O)CCCCCCc1c[nH]c2ccccc12`
ZINC118075337 ZINC	0.788	347.6 Da LogP 4.90 TPSA 55.8	✓ Ro5	✓ Clean	`O=C(O)COc1cc(Cl)ccc1Oc1ccc(Cl)cc1Cl`
ZINC32104 ZINC	0.771	202.3 Da LogP 1.98 TPSA 58.9	✓ Ro5	✓ Clean	`NC(=O)CCCc1c[nH]c2ccccc12`
ZINC1532617 ZINC	0.767	203.2 Da LogP 1.36 TPSA 70.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)Cc1c[nH]c2ccccc12`
ZINC84689016 ZINC	0.767	203.2 Da LogP 1.16 TPSA 70.2	✓ Ro5	✓ Clean	`O=C(O)Cc1c[nH]c2ccccc2c1=O`
ZINC534637094 ZINC	0.765	267.3 Da LogP 3.17 TPSA 73.3	✓ Ro5	✓ Clean	`O=C(O)Cc1c[nH]c2ccc(-c3ccc(O)cc3)cc12`
ZINC142868 ZINC	0.750	265.5 Da LogP 2.57 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)COc1ccc(Cl)cc1Br`
ZINC5784649 ZINC	0.743	278.1 Da LogP 1.57 TPSA 75.6	✓ Ro5	✓ Clean	`O=C(O)CNC(=O)COc1ccc(Cl)cc1Cl`
ZINC5105069 ZINC	0.742	221.0 Da LogP 2.46 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)COc1cc(Cl)ccc1Cl`
ZINC2382319826 ZINC	0.737	364.4 Da LogP 3.13 TPSA 115.4	✓ Ro5	✓ Clean	`O=C(O)Cc1c[nH]c2ccc(OC(=O)Cc3c[nH]c4ccc(O)cc34)…`
ZINC8879429 ZINC	0.725	260.3 Da LogP 1.69 TPSA 82.2	✓ Ro5	✓ Clean	`O=C(O)CNC(=O)CCCc1c[nH]c2ccccc12`
ZINC142359 ZINC	0.724	221.3 Da LogP 3.40 TPSA 32.9	✓ Ro5	✓ Clean	`O=C(c1ccccc1)c1c[nH]c2ccccc12`
ZINC150743 ZINC	0.719	219.1 Da LogP 2.96 TPSA 26.3	✓ Ro5	✓ Clean	`CC(=O)COc1ccc(Cl)cc1Cl`
ZINC1601873 ZINC	0.719	260.6 Da LogP 1.27 TPSA 93.1	✓ Ro5	✓ Clean	`O=C(O)COc1ccc(OCC(=O)O)c(Cl)c1`
ZINC51195 ZINC	0.719	220.1 Da LogP 1.86 TPSA 52.3	✓ Ro5	✓ Clean	`NC(=O)COc1ccc(Cl)cc1Cl`
ZINC71250382 ZINC	0.719	202.6 Da LogP 1.51 TPSA 66.8	✓ Ro5	✓ Clean	`O=C(O)COc1ccc(O)cc1Cl`
ZINC75880727 ZINC	0.719	204.6 Da LogP 1.94 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)COc1ccc(Cl)cc1F`
ZINC85223864 ZINC	0.719	202.6 Da LogP 1.51 TPSA 66.8	✓ Ro5	✓ Clean	`O=C(O)COc1ccc(Cl)cc1O`
ZINC57380 ZINC	0.706	232.2 Da LogP 0.91 TPSA 82.2	✓ Ro5	✓ Clean	`O=C(O)CNC(=O)Cc1c[nH]c2ccccc12`
ZINC19791604 ZINC	0.704	240.5 Da LogP 1.72 TPSA 82.0	✓ Ro5	✓ Clean	`NC(=O)c1nc(Cl)c(Cl)c(N)c1Cl`
ZINC1508317 ZINC	0.700	292.4 Da LogP 3.81 TPSA 44.9	✓ Ro5	✓ Clean	`O=C(CCCc1c[nH]c2ccccc12)NCc1ccccc1`
ZINC1667532 ZINC	0.697	385.2 Da LogP 3.51 TPSA 93.1	✓ Ro5	✓ Clean	`O=C(O)COc1ccc(Cl)cc1Cc1cc(Cl)ccc1OCC(=O)O`
ZINC1692356 ZINC	0.697	200.6 Da LogP 2.11 TPSA 46.5	✓ Ro5	✓ Clean	`Cc1ccc(OCC(=O)O)c(Cl)c1`
ZINC1696211 ZINC	0.697	249.1 Da LogP 3.24 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)CCCOc1ccc(Cl)cc1Cl`
ZINC1706134 ZINC	0.697	204.6 Da LogP 1.94 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)COc1ccc(F)cc1Cl`
ZINC1732199 ZINC	0.697	312.5 Da LogP 2.41 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)COc1ccc(Cl)cc1I`
ZINC205262 ZINC	0.697	264.3 Da LogP 3.03 TPSA 44.9	✓ Ro5	✓ Clean	`O=C(Cc1c[nH]c2ccccc12)NCc1ccccc1`
ZINC404314 ZINC	0.697	254.1 Da LogP 2.56 TPSA 53.1	✓ Ro5	✓ Clean	`O=C(O)Cc1c[nH]c2ccc(Br)cc12`
ZINC404797 ZINC	0.697	200.6 Da LogP 2.11 TPSA 46.5	✓ Ro5	✓ Clean	`Cc1cc(Cl)ccc1OCC(=O)O`
ZINC6091956 ZINC	0.697	235.1 Da LogP 2.85 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)CCOc1ccc(Cl)cc1Cl`
ZINC64970 ZINC	0.697	265.5 Da LogP 2.57 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)COc1ccc(Br)cc1Cl`
ZINC7604113 ZINC	0.697	230.6 Da LogP 1.50 TPSA 83.8	✓ Ro5	✓ Clean	`O=C(O)COc1ccc(C(=O)O)cc1Cl`
ZINC1875329306 ZINC	0.694	297.1 Da LogP 4.12 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)COc1ccc(-c2cccc(Cl)c2)cc1Cl`
ZINC95936163 ZINC	0.694	205.2 Da LogP 1.59 TPSA 62.3	✓ Ro5	✓ Clean	`COC(=O)Cc1c[nH]c2ccc(O)cc12`
ZINC12296943 ZINC	0.692	430.6 Da LogP 4.23 TPSA 89.8	✓ Ro5	✓ Clean	`O=C(CCCc1c[nH]c2ccccc12)NCCNC(=O)CCCc1c[nH]c2cc…`
ZINC12906057 ZINC	0.692	230.3 Da LogP 2.58 TPSA 36.1	✓ Ro5	✓ Clean	`CN(C)C(=O)CCCc1c[nH]c2ccccc12`
ZINC410211 ZINC	0.692	217.3 Da LogP 2.66 TPSA 42.1	✓ Ro5	✓ Clean	`COC(=O)CCCc1c[nH]c2ccccc12`
ZINC82292866 ZINC	0.692	232.3 Da LogP 1.77 TPSA 65.1	✓ Ro5	✓ Clean	`O=C(O)CCNCCc1c[nH]c2ccccc12`
ZINC1559822 ZINC	0.688	371.5 Da LogP 4.31 TPSA 68.0	✓ Ro5	Alert	`CC[n+]1c(-c2ccccc2)c2cc(NCCCN)ccc2c2ccc(N)cc21`
ZINC1690614 ZINC	0.688	233.2 Da LogP 1.50 TPSA 90.4	✓ Ro5	✓ Clean	`O=C(O)C(Cc1c[nH]c2ccccc12)C(=O)O`
ZINC75880748 ZINC	0.688	204.6 Da LogP 1.94 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)COc1cc(Cl)ccc1F`
ZINC4776283 ZINC	0.686	281.1 Da LogP 4.26 TPSA 26.3	✓ Ro5	✓ Clean	`O=C(COc1ccc(Cl)cc1Cl)c1ccccc1`
ZINC1686261 ZINC	0.677	235.3 Da LogP 3.59 TPSA 32.9	✓ Ro5	✓ Clean	`O=C(Cc1ccccc1)c1c[nH]c2ccccc12`
ZINC265617 ZINC	0.676	236.1 Da LogP 1.88 TPSA 58.6	✓ Ro5	✓ Clean	`O=C(COc1ccc(Cl)cc1Cl)NO`

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.