Protein target profile

PA1315

transcriptional regulator

Genome: NC_002516.2

Gene: PA1315 3D evidence: AlphaFold DB model UniProt Q9I429

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Length 204

Pocket druggability 0.699

Ligand records 52

EC / GO 0 / 4

Target summary

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

4 signals

Strengths

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: PA1315
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA1315
Status: annotated
Amino acids: 204
3D evidence: AlphaFold DB model

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:0000976 Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon. GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

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 0.699

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MPDRHAEQPARQPRTKPAEVRLEELMAAAQQLFLDKGVDATTISDIVAAAGVAKGTFYHYFQAKTDILLALRERFTQAFQQRIANAVEACPANDHPGRLRAWTESGLAGYLEGYRLHDVVYSEHHHHQRGNQERDRVLEQLAELLENGAAAGAWPLRNPRLNALLLYSGLHGAADDAIAGGRLDTQPLAGELADAFLRLLGASD

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (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:0000976 Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
37	68	ProSitePatterns	PS01081	TetR-type HTH domain signature.
37	68	InterPro	IPR023772	DNA-binding HTH domain, TetR-type, conserved site
9	65	Gene3D	G3DSA:1.10.10.60	-
97	201	SUPERFAMILY	SSF48498	Tetracyclin repressor-like, C-terminal domain
97	201	InterPro	IPR036271	Tetracyclin repressor-like, C-terminal domain superfamily
66	201	Gene3D	G3DSA:1.10.357.10	Tetracycline Repressor, domain 2
11	89	SUPERFAMILY	SSF46689	Homeodomain-like
11	89	InterPro	IPR009057	Homeobox-like domain superfamily
25	71	Pfam	PF00440	Bacterial regulatory proteins, tetR family
25	71	InterPro	IPR001647	DNA-binding HTH domain, TetR-type
127	147	Coils	Coil	Coil
46	69	PRINTS	PR00455	TetR bacterial regulatory protein HTH signature
46	69	InterPro	IPR001647	DNA-binding HTH domain, TetR-type
25	38	PRINTS	PR00455	TetR bacterial regulatory protein HTH signature
25	38	InterPro	IPR001647	DNA-binding HTH domain, TetR-type
19	79	ProSiteProfiles	PS50977	TetR-type HTH domain profile.
19	79	InterPro	IPR001647	DNA-binding HTH domain, TetR-type
8	202	PANTHER	PTHR30055	HTH-TYPE TRANSCRIPTIONAL REGULATOR RUTR

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.

Loading 3D structure...

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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 PA1315	AlphaFold DB	—	—	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
1				0.699

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 51 0 PAINS alerts

Best available ligand signal

DAO PDB via homolog 200.3 Da · LogP 3.99 · TPSA 37.3 Open detail RCSB PDB

Detail RCSB PDB DAO PDB via homolog

Detail RCSB PDB DCC PDB via homolog

Detail ZINC ZINC1529498 ZINC proposed compound · Tanimoto 1.000

Detail ZINC ZINC1530417 ZINC proposed compound · Tanimoto 1.000

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
DAO RCSB PDB	3ANP	Q5SM42	200.3 Da LogP 3.99 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)O`
DCC RCSB PDB	3ANG	Q5SM42	949.8 Da LogP 2.59 TPSA 363.6	3 viol.	✓ Clean	`CCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)…`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC1529498 ZINC	1.000	200.3 Da LogP 3.99 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)O`
ZINC1530417 ZINC	1.000	228.4 Da LogP 4.77 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)O`
ZINC1628119 ZINC	1.000	214.3 Da LogP 4.38 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)O`
ZINC138457918 ZINC	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCC(=O)O`
ZINC138458029 ZINC	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCC(=O)O`
ZINC144395054 ZINC	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCC(=O)O`
ZINC14619628 ZINC	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCCCC(=O)O`
ZINC196749828 ZINC	0.850	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCC(=O)O`
ZINC2113934076 ZINC	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCC(=O)O`
ZINC2113934082 ZINC	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCC(=O)O`
ZINC2113934083 ZINC	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCC(=O)O`
ZINC2243670 ZINC	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCC(=O)O`
ZINC2569203 ZINC	0.850	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCC(=O)O`
ZINC4798470 ZINC	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCCC(=O)O`
ZINC5973005 ZINC	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCC(=O)O`
ZINC71418182 ZINC	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCC(=O)CCCCC(=O)O`
ZINC79244776 ZINC	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCCC(=O)O`
ZINC86037082 ZINC	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCCC(=O)O`
ZINC86037089 ZINC	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCCCC(=O)O`
ZINC86039283 ZINC	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCC(=O)O`
ZINC3160730 ZINC	0.810	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCC(=O)O`
ZINC4582907 ZINC	0.810	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCC(=O)O`
ZINC4727003 ZINC	0.810	312.4 Da LogP 4.69 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCC(=O)CCCCCCCC(=O)O`
ZINC86037074 ZINC	0.810	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)CCCC(=O)O`
ZINC2378801 ZINC	0.800	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCC(=O)O`
ZINC2113934081 ZINC	0.762	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCCCCCC(=O)O`
ZINC2243668 ZINC	0.762	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCC(=O)O`
ZINC2378799 ZINC	0.762	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCC(=O)O`
ZINC33820423 ZINC	0.762	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCCCC(=O)O`
ZINC2387442 ZINC	0.739	246.4 Da LogP 4.34 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCSCCCCC(=O)O`
ZINC31778284 ZINC	0.739	310.4 Da LogP 4.47 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)/C=C\C(=O)CCCCCCCC(=O)O`
ZINC5540108 ZINC	0.739	310.4 Da LogP 4.47 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)/C=C/C(=O)CCCCCCCC(=O)O`
ZINC64633397 ZINC	0.739	226.4 Da LogP 4.55 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCC(=O)O`
ZINC59545317 ZINC	0.727	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCC(=O)O`
ZINC59545320 ZINC	0.727	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)CCC(=O)O`
ZINC59545336 ZINC	0.727	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCC(=O)O`
ZINC100243318 ZINC	0.708	306.5 Da LogP 3.80 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCCCS(=O)(=O)CCCCCCC(=O)O`
ZINC102184035 ZINC	0.708	272.4 Da LogP 4.52 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCC[C@H](O)CCCCCCC(=O)O`
ZINC158321135 ZINC	0.708	286.5 Da LogP 4.91 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCC[C@H](O)CCCCCCC(=O)O`
ZINC2008597 ZINC	0.708	216.3 Da LogP 2.96 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCC[C@H](O)CCCCC(=O)O`
ZINC2008598 ZINC	0.708	216.3 Da LogP 2.96 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCC[C@@H](O)CCCCC(=O)O`
ZINC33820346 ZINC	0.708	316.5 Da LogP 4.27 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCC[C@H](O)[C@@H](O)CCCCCCCCCCC(=O)O`
ZINC33822254 ZINC	0.708	216.3 Da LogP 2.96 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCC[C@@H](O)CCCCCC(=O)O`
ZINC33822296 ZINC	0.708	286.5 Da LogP 4.91 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCC[C@H](O)CCCCCCCCCCC(=O)O`
ZINC4410616 ZINC	0.708	344.4 Da LogP 2.63 TPSA 111.9	✓ Ro5	✓ Clean	`CCCCCCC(=O)[C@H](O)[C@@H](O)C(=O)CCCCCCCC(=O)O`
ZINC59200967 ZINC	0.708	272.4 Da LogP 4.52 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCC[C@H](O)CCCCCCCC(=O)O`
ZINC59200971 ZINC	0.708	272.4 Da LogP 4.52 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCC[C@@H](O)CCCCCCC(=O)O`
ZINC59200973 ZINC	0.708	272.4 Da LogP 4.52 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCC[C@H](O)CCCCCC(=O)O`
ZINC59724711 ZINC	0.708	244.4 Da LogP 3.74 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCC[C@H](O)CCCCCC(=O)O`
ZINC85857782 ZINC	0.708	286.5 Da LogP 4.91 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCC[C@@H](O)CCCCCCC(=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.