Protein target profile

PA2896

RNA polymerase sigma factor

Genome: NC_002516.2

Gene: PA2896 3D evidence: AlphaFold DB model UniProt Q9HZV1
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Length 194
Pocket druggability 0.713
Ligand records 51
EC / GO 0 / 5
Target summary

Promising target candidate with multiple supporting evidence streams.

5 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 Ligand evidence via structure/bioactivity 1 structural and 0 bioactivity records.

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.
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
PA2896
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA2896
Status
annotated
Amino acids
194
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:0016987 Sigma factors act as the promoter specificity subunit of eubacterial and plant plastid multisubunit RNA polymerases, whose core subunit composition is often described as alpha(2)-beta-beta-prime. Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, the sigma factor binds specifically to promoter elements. The sigma subunit is released once elongation begins. GO:0006352 The initial step of transcription, consisting of the assembly of the RNA polymerase preinitiation complex (PIC) at a gene promoter, as well as the formation of the first few bonds of the RNA transcript. Transcription initiation includes abortive initiation events, which occur when the first few nucleotides are repeatedly synthesized and then released, and ends when promoter clearance takes place. GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. 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.

Target profile

Computed evidence for target prioritization.

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

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 0.713
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MHASTSATTAAGSDETLLARYRKGDSAAFEVLYQRHRQGLYRFLCGLAGQTELADEIYQETWLSLIRSESQPQGRASFRTWLYQIARNRLIDHWRKHGQRQPLQDSYDEQLHAQPDQGAGPEQQLSLSRDGERLQSALETLPEEQREVFLMRAHGELELAEIATLTQSPLETVKSRFRYAVQKLRRLLAEEVAV

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:0016987 Sigma factors act as the promoter specificity subunit of eubacterial and plant plastid multisubunit RNA polymerases, whose core subunit composition is often described as alpha(2)-beta-beta-prime. Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, the sigma factor binds specifically to promoter elements. The sigma subunit is released once elongation begins.
  • GO:0006352 The initial step of transcription, consisting of the assembly of the RNA polymerase preinitiation complex (PIC) at a gene promoter, as well as the formation of the first few bonds of the RNA transcript. Transcription initiation includes abortive initiation events, which occur when the first few nucleotides are repeatedly synthesized and then released, and ends when promoter clearance takes place.
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
13 115 SUPERFAMILY SSF88946 Sigma2 domain of RNA polymerase sigma factors
13 115 InterPro IPR013325 RNA polymerase sigma factor, region 2
115 190 SUPERFAMILY SSF88659 Sigma3 and sigma4 domains of RNA polymerase sigma factors
115 190 InterPro IPR013324 RNA polymerase sigma factor, region 3/4-like
132 185 CDD cd06171 Sigma70_r4
132 184 Pfam PF08281 Sigma-70, region 4
132 184 InterPro IPR013249 RNA polymerase sigma factor 70, region 4 type 2
32 98 Pfam PF04542 Sigma-70 region 2
32 98 InterPro IPR007627 RNA polymerase sigma-70 region 2
126 192 Gene3D G3DSA:1.10.10.10 -
126 192 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
102 131 MobiDBLite mobidb-lite consensus disorder prediction
28 187 NCBIfam TIGR02937 sigma-70 family RNA polymerase sigma factor
28 187 InterPro IPR014284 RNA polymerase sigma-70 like domain
10 190 PANTHER PTHR43133 RNA POLYMERASE ECF-TYPE SIGMA FACTO
10 190 InterPro IPR039425 RNA polymerase sigma-70 like
7 118 Gene3D G3DSA:1.10.1740.10 -
104 131 MobiDBLite mobidb-lite consensus disorder prediction

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 PA2896
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
0.713
Show in viewer
Site 2 FPocket #3
0.208
Show in viewer

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.

51 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 51 via homologs
Structural ligands 1 0 loaded crystals
Bioactive compounds 0 50 ZINC proposed compounds
Drug-like & clean 50 1 PAINS alerts
Best available ligand signal
NCA PDB via homolog 122.1 Da · LogP 0.18 · TPSA 56.0 Open detail RCSB PDB
Detail RCSB PDB NCA PDB via homolog
Detail ZINC ZINC1592410 ZINC proposed compound · Tanimoto 0.708
Detail ZINC ZINC116431 ZINC proposed compound · Tanimoto 0.636
Detail ZINC ZINC10030294 ZINC proposed compound · Tanimoto 0.618

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
NCA RCSB PDB
6IN7
Q06198 122.1 Da LogP 0.18 TPSA 56.0 ✓ Ro5 ✓ Clean c1cc(cnc1)C(=O)N

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.