Protein target profile

PA2016

liu genes regulator

Genome: NC_002516.2

Gene: PA2016 liuR 3D evidence: AlphaFold DB model UniProt Q9I295
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Length 134
Pocket druggability 0.715
EC / GO 0 / 5
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

4 signals

Strengths

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Strong predicted binding pocket FPocket selected-pocket score 0.71. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model

Risks / watch

No major risk signal surfaced in the loaded evidence.

Missing evidence

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. No ligand evidence No experimental PDB ligands, measured ChEMBL bioactivity, or proposed ZINC compound records are available.
How to read 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 TPW 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.

Overview

Basic information about this protein and its source genome.

Accession
PA2016
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA2016 liuR
Status
annotated
Amino acids
134
3D evidence
AlphaFold DB model
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:0008300 The chemical reactions and pathways resulting in the breakdown of an isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues. GO:0045892 Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. 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 pocket evidence

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 0.715
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MSITYTISDLARELDITTRAIRFYEEQGLLSPERRGQERIYSPRDKVSLKLILRGKRIGFSLAECRELIELYDPDPSSGNQKQLNTMLEKIAERRAQLEQQLLDIEQMQLELDTAEERCRAALIKSYNKHTVET

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • 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:0008300 The chemical reactions and pathways resulting in the breakdown of an isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
  • GO:0045892 Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
  • 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.

17 records
Show feature table
Start End DB Term Name
5 72 SMART SM00422 merrmega3
5 72 InterPro IPR000551 MerR-type HTH domain
8 30 ProSitePatterns PS00552 MerR-type HTH domain signature.
8 30 InterPro IPR000551 MerR-type HTH domain
5 70 Pfam PF13411 MerR HTH family regulatory protein
5 70 InterPro IPR000551 MerR-type HTH domain
5 123 CDD cd04776 HTH_GnyR
2 126 Gene3D G3DSA:1.10.1660.10 -
81 125 Coils Coil Coil
1 122 FunFam G3DSA:1.10.1660.10:FF:000015 Transcriptional regulator, MerR family
1 122 PANTHER PTHR30204 REDOX-CYCLING DRUG-SENSING TRANSCRIPTIONAL ACTIVATOR SOXR
1 122 InterPro IPR047057 MerR transcriptional regulator
7 27 Coils Coil Coil
5 121 SUPERFAMILY SSF46955 Putative DNA-binding domain
5 121 InterPro IPR009061 Putative DNA-binding domain superfamily
4 71 ProSiteProfiles PS50937 MerR-type HTH domain profile.
4 71 InterPro IPR000551 MerR-type HTH domain

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.

3D visualization script Full viewer

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Structural evidence

0 + 1

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 PA2016
AlphaFold DB — — full sequence — Viewing
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
0.715
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