Protein profile

PA2054

DNA-binding transcriptional regulator CynR

Genome: NC_002516.2

Gene: cynR PA2054 Structure source: AlphaFold UniProt Q9I261
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Amino acids 295
Annotations 4
Features 21
PDB binders 7
Druggability 0.529

Overview

Basic information about this protein and its source genome.

Accession
PA2054
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
cynR PA2054
Status
annotated
Amino acids
295
Structure source
AlphaFold
GO
GO:0032993 A macromolecular complex containing both protein and DNA molecules. 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:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

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 0.529
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • GO:0032993 A macromolecular complex containing both protein and DNA molecules.
  • 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: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.

21 records
Show feature table
Start End DB Term Name
93 293 Gene3D G3DSA:3.40.190.290 -
1 91 Gene3D G3DSA:1.10.10.10 -
1 91 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
88 284 Pfam PF03466 LysR substrate binding domain
88 284 InterPro IPR005119 LysR, substrate-binding
3 62 Pfam PF00126 Bacterial regulatory helix-turn-helix protein, lysR family
3 62 InterPro IPR000847 Transcription regulator HTH, LysR
68 88 Coils Coil Coil
90 292 SUPERFAMILY SSF53850 Periplasmic binding protein-like II
1 58 ProSiteProfiles PS50931 LysR-type HTH domain profile.
1 58 InterPro IPR000847 Transcription regulator HTH, LysR
1 84 FunFam G3DSA:1.10.10.10:FF:000001 LysR family transcriptional regulator
18 29 PRINTS PR00039 LysR bacterial regulatory protein HTH signature
18 29 InterPro IPR000847 Transcription regulator HTH, LysR
29 39 PRINTS PR00039 LysR bacterial regulatory protein HTH signature
29 39 InterPro IPR000847 Transcription regulator HTH, LysR
39 50 PRINTS PR00039 LysR bacterial regulatory protein HTH signature
39 50 InterPro IPR000847 Transcription regulator HTH, LysR
3 109 SUPERFAMILY SSF46785 Winged helix DNA-binding domain
3 109 InterPro IPR036390 Winged helix DNA-binding domain superfamily
1 287 PANTHER PTHR30419 HTH-TYPE TRANSCRIPTIONAL REGULATOR YBHD

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

0 + 1

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA2054
AlphaFold — — full sequence — Viewing
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 0.529

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.

57 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
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
MLI
4IHS
O68014 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
OAS
4LQ2
P06614 147.1 Da LogP -1.04 TPSA 89.6 ✓ Ro5 ✓ Clean CC(=O)OC[C@@H](C(=O)O)N
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
SAC
4M4G
P06614 147.1 Da LogP -1.43 TPSA 86.6 ✓ Ro5 ✓ Clean CC(=O)N[C@@H](CO)C(=O)O
SKM
5TED
Q8Y9N7 174.2 Da LogP -1.52 TPSA 98.0 ✓ Ro5 ✓ Clean C1[C@H]([C@@H]([C@@H](C=C1C(=O)O)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.