Protein profile

PA4109

transcriptional regulator AmpR

Genome: NC_002516.2

Gene: ampR PA4109 Structure source: Experimental + AlphaFold UniProt P24734
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Amino acids 296
Annotations 10
Features 23
PDB binders 8
Druggability 0.867

Overview

Basic information about this protein and its source genome.

Accession
PA4109
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
ampR PA4109
Status
annotated
Amino acids
296
Structure source
Experimental + AlphaFold
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 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: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:0006351 The synthesis of an RNA transcript from a DNA template. GO:1900232 Any process that stops, prevents or reduces the frequency, rate or extent of single-species biofilm formation on inanimate substrate.

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 0.867
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

10 GO

Gene Ontology (GO)

10
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • 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: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:0006351 The synthesis of an RNA transcript from a DNA template.
  • GO:1900232 Any process that stops, prevents or reduces the frequency, rate or extent of single-species biofilm formation on inanimate substrate.
  • GO:0050714 Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell.
  • 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:1900378 Any process that activates or increases the frequency, rate or extent of secondary metabolite biosynthetic process.
  • 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.

23 records
Show feature table
Start End DB Term Name
164 259 Gene3D G3DSA:3.40.190.10 -
6 63 ProSiteProfiles PS50931 LysR-type HTH domain profile.
6 63 InterPro IPR000847 Transcription regulator HTH, LysR
8 67 Pfam PF00126 Bacterial regulatory helix-turn-helix protein, lysR family
8 67 InterPro IPR000847 Transcription regulator HTH, LysR
98 285 Gene3D G3DSA:3.40.190.10 -
23 34 PRINTS PR00039 LysR bacterial regulatory protein HTH signature
23 34 InterPro IPR000847 Transcription regulator HTH, LysR
34 44 PRINTS PR00039 LysR bacterial regulatory protein HTH signature
34 44 InterPro IPR000847 Transcription regulator HTH, LysR
44 55 PRINTS PR00039 LysR bacterial regulatory protein HTH signature
44 55 InterPro IPR000847 Transcription regulator HTH, LysR
6 289 PANTHER PTHR30537 HTH-TYPE TRANSCRIPTIONAL REGULATOR
6 89 FunFam G3DSA:1.10.10.10:FF:000038 Glycine cleavage system transcriptional activator
95 285 CDD cd08484 PBP2_LTTR_beta_lactamase
95 285 InterPro IPR037420 HTH-type transcriptional activator AmpR, PBP2
91 289 Pfam PF03466 LysR substrate binding domain
91 289 InterPro IPR005119 LysR, substrate-binding
2 86 SUPERFAMILY SSF46785 Winged helix DNA-binding domain
2 86 InterPro IPR036390 Winged helix DNA-binding domain superfamily
85 289 SUPERFAMILY SSF53850 Periplasmic binding protein-like II
2 87 Gene3D G3DSA:1.10.10.10 -
2 87 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily

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

1 + 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 5MMH
X-ray 2.20 Å A,B,C,D
72.0% 84-296
PDBe RCSB PDBj File
Viewing
AlphaFold PA4109
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
2 0.867

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 7.78 0.412

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.

58 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
1PS
6G1B
Q8NP91 201.2 Da LogP -0.09 TPSA 61.1 ✓ Ro5 ✓ Clean c1cc[n+](cc1)CCCS(=O)(=O)[O-]
AKG
5Y2V
P73862 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
BEZ
2F7A
O68014 122.1 Da LogP 1.38 TPSA 37.3 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)O
FOR
6G1D
Q8NP91 30.0 Da LogP -0.18 TPSA 17.1 ✓ Ro5 ✓ Clean C=O
MLI
4IHS
O68014 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
P33
3FD3
A9CJQ0 326.4 Da LogP -0.93 TPSA 95.8 ✓ Ro5 ✓ Clean C(COCCOCCOCCOCCOCCOCCO)O
PEO
6G1B
Q8NP91 34.0 Da LogP 0.02 TPSA 40.5 ✓ Ro5 ✓ Clean OO
RUB
5Z49
Q9F1R2 310.1 Da LogP -2.50 TPSA 191.0 1 viol. ✓ Clean C([C@H]([C@H](C(=O)COP(=O)(O)O)O)O)OP(=O)(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.