Protein profile

PA3678

transcriptional regulator

Genome: NC_002516.2

Gene: PA3678 Structure source: Experimental + AlphaFold UniProt Q9HXW2

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Amino acids 212

Annotations 8

Features 18

PDB binders 5

Druggability 0.807

Overview

Basic information about this protein and its source genome.

Accession: PA3678
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA3678
Status: annotated
Amino acids: 212
Structure source: Experimental + AlphaFold

GO:0032993 A macromolecular complex containing both protein and DNA molecules. 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:0001217 A DNA-binding transcription factor activity that represses or decreases the transcription of specific gene sets. 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: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:0045892 Any process that stops, prevents, or reduces 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 Druggability evidence

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.807

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

GO:0032993 A macromolecular complex containing both protein and DNA molecules.
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:0001217 A DNA-binding transcription factor activity that represses or decreases the transcription of specific gene sets.
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: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: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.
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
12	92	SUPERFAMILY	SSF46689	Homeodomain-like
12	92	InterPro	IPR009057	Homeobox-like domain superfamily
91	202	SUPERFAMILY	SSF48498	Tetracyclin repressor-like, C-terminal domain
91	202	InterPro	IPR036271	Tetracyclin repressor-like, C-terminal domain superfamily
22	68	Pfam	PF00440	Bacterial regulatory proteins, tetR family
22	68	InterPro	IPR001647	DNA-binding HTH domain, TetR-type
15	66	FunFam	G3DSA:1.10.10.60:FF:000141	TetR family transcriptional regulator
11	67	Gene3D	G3DSA:1.10.10.60	-
70	211	Gene3D	G3DSA:1.10.357.10	Tetracycline Repressor, domain 2
16	76	ProSiteProfiles	PS50977	TetR-type HTH domain profile.
16	76	InterPro	IPR001647	DNA-binding HTH domain, TetR-type
43	66	PRINTS	PR00455	TetR bacterial regulatory protein HTH signature
43	66	InterPro	IPR001647	DNA-binding HTH domain, TetR-type
22	35	PRINTS	PR00455	TetR bacterial regulatory protein HTH signature
22	35	InterPro	IPR001647	DNA-binding HTH domain, TetR-type
8	211	PANTHER	PTHR30055	HTH-TYPE TRANSCRIPTIONAL REGULATOR RUTR
93	209	Pfam	PF14246	AefR-like transcriptional repressor, C-terminal domain
93	209	InterPro	IPR039536	Transcriptional regulator TetR, C-terminal, Proteobacteria type

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

1 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 8WRF	X-ray	3.00 Å	A,B	93.4% 15-212	PDBe RCSB PDBj File	Viewing
AlphaFold PA3678	AlphaFold	—	—	full sequence	—	Loaded

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				0.807

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				24.24	0.897

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				0.731

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

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
DCC	1VI0	P94548	949.8 Da LogP 2.59 TPSA 363.6	3 viol.	✓ Clean	`CCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)…`
DG	5K7Z	Q1D4I5	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N…`
IVC	5K7H	Q1D4I5	851.7 Da LogP -0.29 TPSA 363.6	3 viol.	✓ Clean	`CC(C)CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=…`
ST9	3WHC	P94548	1034.0 Da LogP 4.93 TPSA 363.6	3 viol.	✓ Clean	`CCCCCCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C…`
TCH	3QQA	Q7B8P6	515.7 Da LogP 2.37 TPSA 144.2	1 viol.	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@@H]2[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
ZINC12296728	1.000	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@@H](O)[C@@H](COP(=O)(O)O)…`
ZINC13527599	1.000	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@@H](O)[C@@H](COP(=O)(O)O…`
ZINC13527603	1.000	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@@H](COP(=O)(O)O)…`
ZINC1532627	1.000	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@@H](O)[C@H](COP(=O)(O)O)…`
ZINC1730395	1.000	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O…`
ZINC3869846	1.000	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@H](COP(=O)(O)O)O…`
ZINC3869847	1.000	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2…`
ZINC3869848	1.000	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O…`
ZINC12503703	0.860	427.2 Da LogP -1.42 TPSA 232.3	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@@H](CO[P@@](=O)(…`
ZINC8215878	0.860	427.2 Da LogP -1.42 TPSA 232.3	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O…`
ZINC118914627	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@H]2[C@@H…`
ZINC118915233	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@H]2[C@H…`
ZINC118915234	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@H]2[C@H]…`
ZINC118915235	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@H]2[C@@…`
ZINC13515755	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@@H]2[C@@…`
ZINC14984492	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@@H]2[C@H…`
ZINC1857687	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@@H]1CC[C@H]2[C@@…`
ZINC1857777820	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@@H]1CC[C@H]2[C@H…`
ZINC1857777821	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@@H](CCC(=O)NCCS(=O)(=O)O)[C@@H]1CC[C@H]2[C@…`
ZINC1888841	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@@H]1CC[C@H]2[C@H…`
ZINC1889002139	0.813	449.7 Da LogP 3.89 TPSA 89.8	✓ Ro5	✓ Clean	`CCCNC(=O)CC[C@@H](C)[C@H]1CC[C@@H]2[C@H]3[C@H](…`
ZINC1889002140	0.813	449.7 Da LogP 3.89 TPSA 89.8	✓ Ro5	✓ Clean	`CCCNC(=O)CC[C@@H](C)[C@H]1CC[C@@H]2[C@H]3[C@H](…`
ZINC1889002141	0.813	449.7 Da LogP 3.89 TPSA 89.8	✓ Ro5	✓ Clean	`CCCNC(=O)CC[C@@H](C)[C@H]1CC[C@@H]2[C@@H]3[C@H]…`
ZINC1889002142	0.813	449.7 Da LogP 3.89 TPSA 89.8	✓ Ro5	✓ Clean	`CCCNC(=O)CC[C@@H](C)[C@H]1CC[C@@H]2[C@@H]3[C@H]…`
ZINC252584587	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@@H]1CC[C@@H]2[C@…`
ZINC253534622	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@@H]1CC[C@@H]2[C@…`
ZINC253534623	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@@H](CCC(=O)NCCS(=O)(=O)O)[C@@H]1CC[C@@H]2[C…`
ZINC253534624	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@@H](CCC(=O)NCCS(=O)(=O)O)[C@@H]1CC[C@@H]2[C…`
ZINC253558526	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@@H]2[C@@…`
ZINC29552512	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@@H]2[C@H…`
ZINC33650236	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@H]2[C@H]…`
ZINC33650237	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@@H]2[C@H…`
ZINC38324520	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@@H]2[C@H…`
ZINC3914813	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@H]2[C@@H…`
ZINC40164308	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@H]2[C@@H…`
ZINC55161741	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@@H]1CC[C@H]2[C@@…`
ZINC5822376	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@H]2[C@H]…`
ZINC58475681	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@H]2[C@H]…`
ZINC60292561	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@H]2[C@@H…`
ZINC60292564	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@@H]2[C@@…`
ZINC85345450	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@@H]2[C@H…`
ZINC8551820	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@@H]2[C@H…`
ZINC91297636	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@H]1CC[C@@H]2[C@@…`
ZINC953115464	0.813	499.7 Da LogP 3.40 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCS(=O)(=O)O)[C@@H]1CC[C@H]2[C@H…`
ZINC118912564	0.790	444.6 Da LogP 2.86 TPSA 115.1	✓ Ro5	✓ Clean	`C[C@H](CCS(=O)(=O)O)[C@H]1CC[C@H]2[C@H]3[C@H](C…`
ZINC1857533481	0.790	444.6 Da LogP 2.86 TPSA 115.1	✓ Ro5	✓ Clean	`C[C@@H](CCS(=O)(=O)O)[C@@H]1CC[C@H]2[C@H]3[C@H]…`
ZINC253534390	0.790	444.6 Da LogP 2.86 TPSA 115.1	✓ Ro5	✓ Clean	`C[C@H](CCS(=O)(=O)O)[C@@H]1CC[C@@H]2[C@H]3[C@H]…`
ZINC253534391	0.790	444.6 Da LogP 2.86 TPSA 115.1	✓ Ro5	✓ Clean	`C[C@@H](CCS(=O)(=O)O)[C@@H]1CC[C@@H]2[C@H]3[C@H…`
ZINC253534392	0.790	444.6 Da LogP 2.86 TPSA 115.1	✓ Ro5	✓ Clean	`C[C@@H](CCS(=O)(=O)O)[C@@H]1CC[C@@H]2[C@H]3[C@H…`
ZINC253534393	0.790	444.6 Da LogP 2.86 TPSA 115.1	✓ Ro5	✓ Clean	`C[C@H](CCS(=O)(=O)O)[C@@H]1CC[C@@H]2[C@H]3[C@H]…`

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.