Protein profile
VK055_4553
bacterial regulatory helix-turn-helix, AraC family protein
Genome: KpATCC43816
Overview
Basic information about this protein and its source genome.
- Accession
- VK055_4553
- Gene
- AIK83091.1 rarA
- Status
- annotated
- Amino acids
- 120
- Structure source
- AlphaFold + ColabFold
Target profile
Computed evidence for target prioritization.
- Human off-target
- No hit
- Human identity (%)
- 0.0
- Gut microbiome off-target
- hit
- Essential (DEG)
- Y
- DEG identity (%)
- 48.077
- DEG E-value
- 1.5e-32
- Localization
- Cytoplasmic
- ColabFold pLDDT
- 90.82
Selected Druggability evidence
AlphaFold / UniProt modelSelected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.
Sequence
Primary amino-acid sequence viewer.
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Gene Ontology (GO)
3- 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: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.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 88 | 104 | PRINTS | PR00032 | AraC bacterial regulatory protein HTH signature |
| 88 | 104 | InterPro | IPR020449 | Transcription regulator HTH, AraC- type |
| 73 | 88 | PRINTS | PR00032 | AraC bacterial regulatory protein HTH signature |
| 73 | 88 | InterPro | IPR020449 | Transcription regulator HTH, AraC- type |
| 8 | 106 | ProSiteProfiles | PS01124 | Bacterial regulatory proteins, araC family DNA-binding domain profile. |
| 8 | 106 | InterPro | IPR018060 | DNA binding HTH domain, AraC-type |
| 56 | 117 | Gene3D | G3DSA:1.10.10.60 | - |
| 21 | 104 | SMART | SM00342 | aracneu4 |
| 21 | 104 | InterPro | IPR018060 | DNA binding HTH domain, AraC-type |
| 58 | 108 | SUPERFAMILY | SSF46689 | Homeodomain-like |
| 58 | 108 | InterPro | IPR009057 | Homeobox-like domain superfamily |
| 5 | 55 | Gene3D | G3DSA:1.10.10.60 | - |
| 6 | 55 | SUPERFAMILY | SSF46689 | Homeodomain-like |
| 6 | 55 | InterPro | IPR009057 | Homeobox-like domain superfamily |
| 3 | 113 | PANTHER | PTHR47504 | RIGHT ORIGIN-BINDING PROTEIN |
| 55 | 100 | ProSitePatterns | PS00041 | Bacterial regulatory proteins, araC family signature. |
| 55 | 100 | InterPro | IPR018062 | HTH domain AraC-type, conserved site |
| 27 | 105 | Pfam | PF12833 | Helix-turn-helix domain |
| 27 | 105 | InterPro | IPR018060 | DNA binding HTH domain, AraC-type |
3D Structure
Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.
No pockets are loaded yet for the displayed AlphaFold model AF_A0A0W7ZYE8 structure. Run experimental pocket backfill to show FPocket/P2Rank overlays on this structure.
Loading 3D structure...
Structural evidence
0 + 2Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold
AF_A0A0W7ZYE8
|
AlphaFold | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_4553
|
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.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, 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 |
|---|---|---|---|---|---|---|
| BTB | Q92A04 | 209.2 Da LogP -3.01 TPSA 104.4 | ✓ Ro5 | ✓ Clean |
C(CO)N(CCO)C(CO)(CO)CO
|
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 |
|---|---|---|---|---|---|
| ZINC1615342 | 1.000 | 209.2 Da LogP -3.01 TPSA 104.4 | ✓ Ro5 | ✓ Clean |
OCCN(CCO)C(CO)(CO)CO
|
| ZINC2334905 | 0.522 | 261.4 Da LogP 1.10 TPSA 63.9 | ✓ Ro5 | ✓ Clean |
CC(C)CCN(CCC(C)C)C(CO)(CO)CO
|
| ZINC3159953 | 0.522 | 261.4 Da LogP 1.38 TPSA 63.9 | ✓ Ro5 | ✓ Clean |
CCCCCN(CCCCC)C(CO)(CO)CO
|
| ZINC5297554 | 0.500 | 289.5 Da LogP 2.16 TPSA 63.9 | ✓ Ro5 | ✓ Clean |
CCCCCCN(CCCCCC)C(CO)(CO)CO
|
| ZINC97941822 | 0.500 | 317.5 Da LogP 2.94 TPSA 63.9 | ✓ Ro5 | ✓ Clean |
CCCCCCCN(CCCCCCC)C(CO)(CO)CO
|
| ZINC97942927 | 0.500 | 373.6 Da LogP 4.51 TPSA 63.9 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCN(CCCCCCCCC)C(CO)(CO)CO
|
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.