Protein target profile

PA2123

transcriptional regulator

Genome: NC_002516.2

Gene: PA2123 3D evidence: AlphaFold DB model UniProt Q9I1Z2
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Length 310
Pocket druggability 0.712
Ligand records 55
EC / GO 0 / 4
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 5 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
PA2123
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA2123
Status
annotated
Amino acids
310
3D evidence
AlphaFold DB model
GO
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: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 0.712
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MNKFAEMTTFVSVVDAHSFSEAARRLGTTKSQVSQRIQQLERRLGRVLLNRTRPLSLTDPGRTYYEHACRLLQELEQAEASVLDADDDLRGQLRLSAPLAFTPRYLAPLLARFAERHPQLRVDVQADDRFVNLQEPRFDMALRMGRLDDSCLVARPITANRHLLCASPDYLARHGVPQHPEELQAHDGLVYYNREPGGMLCLPVDGEPASFRIRVRMRTDSGHQLLEGARAGLGLAILPSFLAADALLAGELLPVLPGYSPDGGQVSVVYRKTQRTPRKILVLGQFLEEEIGDPAPWDRALIERGLLPPG

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • 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: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.

16 records
Show feature table
Start End DB Term Name
87 294 SUPERFAMILY SSF53850 Periplasmic binding protein-like II
2 85 Gene3D G3DSA:1.10.10.10 -
2 85 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
91 287 CDD cd08422 PBP2_CrgA_like
1 58 ProSiteProfiles PS50931 LysR-type HTH domain profile.
1 58 InterPro IPR000847 Transcription regulator HTH, LysR
23 43 Coils Coil Coil
6 111 SUPERFAMILY SSF46785 Winged helix DNA-binding domain
6 111 InterPro IPR036390 Winged helix DNA-binding domain superfamily
5 291 PANTHER PTHR30537 HTH-TYPE TRANSCRIPTIONAL REGULATOR
88 290 Pfam PF03466 LysR substrate binding domain
88 290 InterPro IPR005119 LysR, substrate-binding
86 290 Gene3D G3DSA:3.40.190.290 -
1 84 FunFam G3DSA:1.10.10.10:FF:000001 LysR family transcriptional regulator
6 62 Pfam PF00126 Bacterial regulatory helix-turn-helix protein, lysR family
6 62 InterPro IPR000847 Transcription regulator HTH, LysR

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 PA2123
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
0.712
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.

55 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 55 via homologs
Structural ligands 5 0 loaded crystals
Bioactive compounds 0 50 ZINC proposed compounds
Drug-like & clean 38 2 PAINS alerts
Best available ligand signal
BEZ PDB via homolog 122.1 Da · LogP 1.38 · TPSA 37.3 Open detail RCSB PDB
Detail RCSB PDB BEZ PDB via homolog
Detail RCSB PDB CCU PDB via homolog
Detail RCSB PDB MLI PDB via homolog
Detail RCSB PDB P33 PDB via homolog

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
BEZ RCSB PDB
2F7A
O68014 122.1 Da LogP 1.38 TPSA 37.3 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)O
CCU RCSB PDB
3GLB
P07774 142.1 Da LogP 0.27 TPSA 74.6 ✓ Ro5 ✓ Clean C(=C/C(=O)O)/C=C\C(=O)O
MLI RCSB PDB
4IHS
O68014 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
P33 RCSB PDB
3FD3
A9CJQ0 326.4 Da LogP -0.93 TPSA 95.8 ✓ Ro5 ✓ Clean C(COCCOCCOCCOCCOCCOCCO)O
RUB RCSB PDB
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.