Protein target profile

VK055_0605

bacterial regulatory, tetR family protein

Genome: KpATCC43816 Gene: AIK79228.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GU13

Export view

Length 191

Pocket druggability 0.997

Direct ligand evidence 0 16 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

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: 1.0% 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.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 93.95 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 0.997

Structure A0A0H3GU13

Pocket Pocket 1

P2Rank 0.848

Structure A0A0H3GU13

Pocket Pocket 1

ColabFold model

FPocket 0.717 · Pocket 1

P2Rank 0.9 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 48 / 4744 genomes with a hit

Prevalence 1.0%

Cross-references

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

Sequence

UniProt A0A0H3GU13

Sequence

Primary amino-acid sequence viewer.

MHYLQRDARREGIMQAAMRLALRGGFAAMTVRQIAREAQVAAGQLHHHFTSIGELKAQVFIRLIREMLDMPLVAEDASWRERLFSMIGSEDGRLEPYIRLWREGQVLADSDPDIKAAYLLTMNMWHAETVAIIEQGLASGEFRSAEPAADIAWRFIALVCGLDGIYALDAQALDEAAFSRYVNKMITLELF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

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

12 records

Show feature table

Start	End	DB	Term	Name
6	191	Gene3D	G3DSA:1.10.357.10	Tetracycline Repressor, domain 2
5	178	PANTHER	PTHR30055	HTH-TYPE TRANSCRIPTIONAL REGULATOR RUTR
13	55	Pfam	PF00440	Bacterial regulatory proteins, tetR family
13	55	InterPro	IPR001647	DNA-binding HTH domain, TetR-type
79	176	SUPERFAMILY	SSF48498	Tetracyclin repressor-like, C-terminal domain
79	176	InterPro	IPR036271	Tetracyclin repressor-like, C-terminal domain superfamily
98	186	Pfam	PF13977	BetI-type transcriptional repressor, C-terminal
98	186	InterPro	IPR039538	BetI-type transcriptional repressor, C-terminal
7	67	ProSiteProfiles	PS50977	TetR-type HTH domain profile.
7	67	InterPro	IPR001647	DNA-binding HTH domain, TetR-type
4	70	SUPERFAMILY	SSF46689	Homeodomain-like
4	70	InterPro	IPR009057	Homeobox-like domain superfamily

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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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 #1

0.997

Likely same site as P2Rank 1 4.2 Å 17 shared residues 81% of smaller site

Unusual size

Show in viewer

Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1

0.848

Likely same site as FPocket 1 4.2 Å 17 shared residues 81% of smaller site

Show in viewer

Surrounding area

Site 2 P2Rank #2

0.042

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_A0A0H3GU13	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_0605	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.

16 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 12 similarity-based ZINC candidates

Best available ligand signal

B3P PDB via homolog 282.3 Da · LogP -4.01 · TPSA 145.4 Open detail RCSB PDB

BEN PDB via homolog Detail RCSB PDB

CHT PDB via homolog Detail RCSB PDB

KEN PDB via homolog Detail RCSB PDB

ZINC4521259 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
B3P RCSB PDB	4ICH	C7MT25	282.3 Da LogP -4.01 TPSA 145.4	1 viol.	✓ Clean	`C(CNC(CO)(CO)CO)CNC(CO)(CO)CO`
BEN RCSB PDB	4JNN	C7MT25	120.2 Da LogP 0.97 TPSA 49.9	✓ Ro5	✓ Clean	`[H]/N=C(\c1ccccc1)/N`
CHT RCSB PDB	4KWA	C7MT25	104.2 Da LogP -0.32 TPSA 20.2	✓ Ro5	✓ Clean	`C[N+](C)(C)CCO`
KEN RCSB PDB	4NEL	C7MT25	59.1 Da LogP 0.18 TPSA 3.2	✓ Ro5	✓ Clean	`CN(C)C`

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
ZINC4521259 ZINC	1.000	282.3 Da LogP -4.01 TPSA 145.4	1 viol.	✓ Clean	`OCC(CO)(CO)NCCCNC(CO)(CO)CO`
ZINC115591405 ZINC	0.636	373.6 Da LogP 4.55 TPSA 72.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCCCCNC(CO)(CO)CO`
ZINC115591837 ZINC	0.636	317.5 Da LogP 2.99 TPSA 72.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCNC(CO)(CO)CO`
ZINC143575268 ZINC	0.636	289.5 Da LogP 2.21 TPSA 72.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC(CO)(CO)CO`
ZINC2322313 ZINC	0.636	233.4 Da LogP 0.65 TPSA 72.7	✓ Ro5	✓ Clean	`CCCCCCCCNC(CO)(CO)CO`
ZINC97996983 ZINC	0.636	345.6 Da LogP 3.77 TPSA 72.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCCNC(CO)(CO)CO`
ZINC1611594 ZINC	0.583	243.3 Da LogP -2.43 TPSA 127.1	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC(CO)(CO)CO`
ZINC5273895 ZINC	0.583	257.3 Da LogP -2.04 TPSA 127.1	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC(CO)(CO)CO`
ZINC100368719 ZINC	0.500	210.3 Da LogP 2.43 TPSA 52.0	✓ Ro5	✓ Clean	`N/C(=C(\N)c1ccccc1)c1ccccc1`
ZINC1530141 ZINC	0.500	229.3 Da LogP -2.82 TPSA 127.1	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC(CO)(CO)CO`
ZINC24716871 ZINC	0.500	210.3 Da LogP 2.43 TPSA 52.0	✓ Ro5	✓ Clean	`N/C(=C(/N)c1ccccc1)c1ccccc1`
ZINC5771971 ZINC	0.500	238.3 Da LogP 1.71 TPSA 76.8	✓ Ro5	✓ Clean	`N/C(=N\N=C(/N)c1ccccc1)c1ccccc1`

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.