Protein profile

PA3477

transcriptional regulator RhlR

Genome: NC_002516.2

Gene: PA3477 vsmR lasM rhlR Structure source: Experimental + AlphaFold UniProt P54292
Amino acids 241
Annotations 16
Features 28
PDB binders 21
Druggability 0.899

Overview

Basic information about this protein and its source genome.

Accession
PA3477
Gene
PA3477 vsmR lasM rhlR
Status
annotated
Amino acids
241
Structure source
Experimental + AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
Cytoplasmic

Selected Druggability evidence

Selected 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.

FPocket 0.899
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

16 GO

Gene Ontology (GO)

16
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0032993 A macromolecular complex containing both protein and DNA molecules.
  • GO:0001216 A DNA-binding transcription factor activity that activates or increases transcription of specific gene sets.
  • 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:0001217 A DNA-binding transcription factor activity that represses or decreases the transcription of specific gene sets.
  • GO:0038023 Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
  • 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.
  • GO:0010467 The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes.
  • GO:0045893 Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0046889 Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.
  • GO:0045862 Any process that activates or increases the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
  • GO:0062162 Any process that increases the frequency, rate or extent of a pyocyanine biosynthetic process.
  • GO:1900378 Any process that activates or increases the frequency, rate or extent of secondary metabolite biosynthetic process.
  • GO:0009372 The cell-cell signaling process in which single-celled organisms carry out coordinated responses by monitoring their own population density, and often also that of other microbes, by producing small, diffusible, signal molecules, detecting the concentration of these molecules, and triggering a signal transduction pathway when a certain threshold is reached. Quorum sensing can occur amongst microbial communities in the environment or within host organisms.
  • 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 Features

Domain/signature hits from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
9 172 SUPERFAMILY SSF75516 Pheromone-binding domain of LuxR-like quorum-sensing transcription factors
9 172 InterPro IPR036693 Transcription factor LuxR-like, autoinducer-binding domain superfamily
26 164 Pfam PF03472 Autoinducer binding domain
26 164 InterPro IPR005143 Transcription factor LuxR-like, autoinducer-binding domain
181 235 Pfam PF00196 Bacterial regulatory proteins, luxR family
181 235 InterPro IPR000792 Transcription regulator LuxR, C-terminal
181 229 CDD cd06170 LuxR_C_like
181 229 InterPro IPR000792 Transcription regulator LuxR, C-terminal
181 195 PRINTS PR00038 LuxR bacterial regulatory protein HTH signature
181 195 InterPro IPR000792 Transcription regulator LuxR, C-terminal
195 211 PRINTS PR00038 LuxR bacterial regulatory protein HTH signature
195 211 InterPro IPR000792 Transcription regulator LuxR, C-terminal
211 223 PRINTS PR00038 LuxR bacterial regulatory protein HTH signature
211 223 InterPro IPR000792 Transcription regulator LuxR, C-terminal
171 241 SUPERFAMILY SSF46894 C-terminal effector domain of the bipartite response regulators
171 241 InterPro IPR016032 Signal transduction response regulator, C-terminal effector
195 222 ProSitePatterns PS00622 LuxR-type HTH domain signature.
195 222 InterPro IPR000792 Transcription regulator LuxR, C-terminal
174 239 ProSiteProfiles PS50043 LuxR-type HTH domain profile.
174 239 InterPro IPR000792 Transcription regulator LuxR, C-terminal
180 241 Gene3D G3DSA:1.10.10.10 -
180 241 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
178 241 FunFam G3DSA:1.10.10.10:FF:000297 DNA-binding transcriptional activator SdiA
3 177 Gene3D G3DSA:3.30.450.80 -
3 177 InterPro IPR036693 Transcription factor LuxR-like, autoinducer-binding domain superfamily
29 240 PANTHER PTHR44688 -
178 235 SMART SM00421 luxrmega5
178 235 InterPro IPR000792 Transcription regulator LuxR, C-terminal

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

6 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 7R3G
X-ray 2.15 Å A,B
100.0% 1-241
Viewing
PDB 7R3J
X-ray 3.06 Å C,D
100.0% 1-241
Loaded
PDB 8B4A
X-ray 3.06 Å C,D
100.0% 1-241
Loaded
PDB 7R3I
X-ray 3.10 Å A,B
100.0% 1-241
Loaded
PDB 7R3E
X-ray 3.46 Å A,B
100.0% 1-241
Loaded
PDB 7R3H
X-ray 3.49 Å A,B,C,D
100.0% 1-241
Loaded
AlphaFold PA3477
AlphaFold full sequence Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
1 0.899

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 23.35 0.888

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.

101 records

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
3M5 A0A0H2Z901 269.3 Da LogP 1.74 TPSA 72.5 ✓ Ro5 ✓ Clean CCCCCCCC(=O)CC(=O)N[C@H]1CCOC1=O
480 Q8XBD0 218.3 Da LogP 1.24 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC(=O)OC[C@H](CO)O
482 Q8XBD0 213.2 Da LogP 0.18 TPSA 72.5 ✓ Ro5 ✓ Clean CCCC(=O)CC(=O)N[C@H]1CCOC1=O
EVY Q9RMS5 339.5 Da LogP 4.76 TPSA 55.4 ✓ Ro5 ✓ Clean CCCCCCCC[C@H](CCCCCC)C(=O)N[C@H]1CCOC1=O
EWM Q9RMS5 283.4 Da LogP 3.34 TPSA 55.4 ✓ Ro5 ✓ Clean CCCCCCCCCCCC(=O)N[C@H]1CCOC1=O
FX7 P25084 556.3 Da LogP 6.32 TPSA 98.5 2 viol. ✓ Clean CCCCCCCC(=O)Oc1c(cc(cc1Br)Br)CNC(=O)c2ccccc2[N+…
FXD P25084 534.2 Da LogP 5.27 TPSA 98.5 2 viol. ✓ Clean c1ccc(cc1)C(=O)Oc2c(cc(cc2Br)Br)CNC(=O)c3ccccc3…
FXJ P25084 564.2 Da LogP 5.28 TPSA 107.8 2 viol. ✓ Clean COc1ccc(cc1)C(=O)Oc2c(cc(cc2Br)Br)CNC(=O)c3cccc…
FXS P25084 579.2 Da LogP 5.18 TPSA 141.7 2 viol. ✓ Clean c1ccc(c(c1)C(=O)NCc2cc(cc(c2OC(=O)c3ccccc3[N+](…
FY1 P25084 474.1 Da LogP 4.03 TPSA 90.7 ✓ Ro5 ✓ Clean COCOc1c(cc(cc1Br)Br)CNC(=O)c2ccccc2[N+](=O)[O-]
FY4 P25084 568.6 Da LogP 5.92 TPSA 98.5 2 viol. ✓ Clean c1ccc(c(c1)C(=O)NCc2cc(cc(c2OC(=O)c3ccc(cc3)Cl)…
FY7 P25084 559.2 Da LogP 5.14 TPSA 122.3 2 viol. ✓ Clean c1ccc(c(c1)C#N)C(=O)Oc2c(cc(cc2Br)Br)CNC(=O)c3c…
FYD P25084 564.2 Da LogP 5.28 TPSA 107.8 2 viol. ✓ Clean COc1ccccc1C(=O)Oc2c(cc(cc2Br)Br)CNC(=O)c3ccccc3…
HTF P07026 227.3 Da LogP 1.78 TPSA 55.4 ✓ Ro5 ✓ Clean CCCCCCCC(=O)N[C@H]1CCOC1=O
K5D P25084 326.2 Da LogP 1.71 TPSA 58.6 ✓ Ro5 ✓ Clean c1cc(cc(c1)Br)OCC(=O)N[C@@H]2C[C@@H]3C[C@@H]3[C…
K5G P25084 358.3 Da LogP 2.76 TPSA 55.4 ✓ Ro5 ✓ Clean c1cc(cc(c1)Br)OCCCC(=O)N[C@H]2CCSC2=O
K5J P25084 351.4 Da LogP 1.34 TPSA 89.5 ✓ Ro5 ✓ Clean CS(=O)(=O)c1cccc(c1)OCCCC(=O)N[C@@H]2C[C@H]3C[C…
K5M P25084 351.4 Da LogP 1.34 TPSA 89.5 ✓ Ro5 ✓ Clean CS(=O)(=O)c1cccc(c1)OCCCC(=O)N[C@H]2C[C@@H]3C[C…
TX3 P25084 537.6 Da LogP 6.32 TPSA 55.4 2 viol. ✓ Clean Cc1ccccc1C(=O)Oc2c(cc(cc2Br)Br)CNC(=O)c3ccccc3Cl
TX7 P25084 613.1 Da LogP 6.03 TPSA 98.5 2 viol. ✓ Clean c1ccc(c(c1)C(=O)NCc2cc(cc(c2OC(=O)c3ccc(cc3)Br)…
TY4 P25084 527.6 Da LogP 6.87 TPSA 55.4 2 viol. ✓ Clean Cc1cc(cc(c1OC(=O)c2ccc(cc2Cl)Cl)CNC(=O)c3ccccc3…

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.