Protein target profile

PA5337

DNA-directed RNA polymerase subunit omega

Genome: NC_002516.2 Gene: PA5337 rpoZ 3D evidence: AlphaFold DB model UniProt Q9HTM1
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Length 88
Pocket druggability 0.718
Ligand records 52
EC / GO 1 / 6
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 0.72. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model Ligand evidence via structure/bioactivity 2 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
PA5337
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA5337 rpoZ
Status
annotated
Amino acids
88
3D evidence
AlphaFold DB model
EC
2.7.7.6
GO
GO:0000345 The eubacterial DNA-directed RNA polymerase is a multisubunit complex with a core composed of the essential subunits beta-prime, beta, and two copies of alpha and a fifth nonessential subunit called omega. An additional subunit, a sigma factor, is required for promoter recognition and specificity. GO:0001000 Binding to a bacterial-type RNA polymerase core enzyme, typically consisting of two alpha, one beta, one beta prime, and one omega subunit. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0003899 Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'. 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:0006351 The synthesis of an RNA transcript from a DNA template.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
Hit
Essential (DEG)
Y
Localization
Unknown

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 0.718
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MARVTVEDCLDNVDNRFELVMLATKRARQLATGGKEPKVAWENDKPTVVALREIASGLVDENVVQQEDIVEDEPLFAAFDDEANTEAL

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0000345 The eubacterial DNA-directed RNA polymerase is a multisubunit complex with a core composed of the essential subunits beta-prime, beta, and two copies of alpha and a fifth nonessential subunit called omega. An additional subunit, a sigma factor, is required for promoter recognition and specificity.
  • GO:0001000 Binding to a bacterial-type RNA polymerase core enzyme, typically consisting of two alpha, one beta, one beta prime, and one omega subunit.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0003899 Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
  • 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:0006351 The synthesis of an RNA transcript from a DNA template.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
2 86 Gene3D G3DSA:3.90.940.10 -
2 86 InterPro IPR036161 RPB6/omega subunit-like superfamily
1 77 SUPERFAMILY SSF63562 RPB6/omega subunit-like
1 77 InterPro IPR036161 RPB6/omega subunit-like superfamily
1 62 Hamap MF_00366 DNA-directed RNA polymerase subunit omega [rpoZ].
1 62 InterPro IPR003716 DNA-directed RNA polymerase, omega subunit
8 59 Pfam PF01192 RNA polymerase Rpb6
8 59 InterPro IPR006110 RNA polymerase, subunit omega/Rpo6/RPB6
1 87 PANTHER PTHR34476 DNA-DIRECTED RNA POLYMERASE SUBUNIT OMEGA
1 87 InterPro IPR003716 DNA-directed RNA polymerase, omega subunit
1 59 NCBIfam TIGR00690 DNA-directed RNA polymerase subunit omega
1 59 InterPro IPR003716 DNA-directed RNA polymerase, omega subunit
8 61 SMART SM01409 RNA_pol_Rpb6_2
8 61 InterPro IPR006110 RNA polymerase, subunit omega/Rpo6/RPB6

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.

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Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #2
0.718
Show in viewer
Site 2 FPocket #1
0.23
Show in viewer
All structural evidence

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 PA5337
AlphaFold DB — — full sequence — Viewing

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.

52 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 52 via homologs
Structural ligands 2 0 loaded crystals
Bioactive compounds 0 50 ZINC proposed compounds
Drug-like & clean 8 0 PAINS alerts
Best available ligand signal
0O2 PDB via homolog 683.1 Da · LogP -2.10 · TPSA 392.2 Open detail RCSB PDB
G4P PDB via homolog Detail RCSB PDB
ZINC104869865 ZINC proposed compound · Tanimoto 0.823 Detail ZINC
ZINC12504289 ZINC proposed compound · Tanimoto 0.823 Detail ZINC
ZINC34541308 ZINC proposed compound · Tanimoto 0.823 Detail ZINC

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
0O2 RCSB PDB
4JK2
P0A800 683.1 Da LogP -2.10 TPSA 392.2 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…
G4P RCSB PDB
4JK1
P0A800 603.2 Da LogP -2.22 TPSA 345.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=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.