Protein profile

PA4878

transcriptional regulator

Genome: NC_002516.2

Gene: brlR PA4878 Structure source: Experimental + AlphaFold UniProt Q9HUT5

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Amino acids 270

Annotations 9

Features 22

PDB binders 15

Druggability 0.795

Overview

Basic information about this protein and its source genome.

Accession: PA4878
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: brlR PA4878
Status: annotated
Amino acids: 270
Structure source: Experimental + AlphaFold

GO:0032993 A macromolecular complex containing both protein and DNA molecules. GO:0001216 A DNA-binding transcription factor activity that activates or increases transcription of specific gene sets. 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:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. 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 0.795

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

9 GO

Gene Ontology (GO)

GO:0032993 A macromolecular complex containing both protein and DNA molecules.
GO:0001216 A DNA-binding transcription factor activity that activates or increases transcription of specific gene sets.
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:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
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:0045893 Any process that activates or increases 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.

22 records

Show feature table

Start	End	DB	Term	Name
1	123	Gene3D	G3DSA:1.10.1660.10	-
1	112	PANTHER	PTHR30204	REDOX-CYCLING DRUG-SENSING TRANSCRIPTIONAL ACTIVATOR SOXR
1	112	InterPro	IPR047057	MerR transcriptional regulator
123	269	Pfam	PF14526	Integron-associated effector binding protein
123	269	InterPro	IPR029441	Integron-associated effector binding protein
2	112	CDD	cd01107	HTH_BmrR
1	71	ProSiteProfiles	PS50937	MerR-type HTH domain profile.
1	71	InterPro	IPR000551	MerR-type HTH domain
124	270	FunFam	G3DSA:3.20.80.10:FF:000016	Probable transcriptional regulator
2	108	SUPERFAMILY	SSF46955	Putative DNA-binding domain
2	108	InterPro	IPR009061	Putative DNA-binding domain superfamily
124	270	Gene3D	G3DSA:3.20.80.10	Regulatory factor, effector binding domain
124	270	InterPro	IPR011256	Regulatory factor, effector binding domain superfamily
120	269	SUPERFAMILY	SSF55136	Probable bacterial effector-binding domain
120	269	InterPro	IPR011256	Regulatory factor, effector binding domain superfamily
2	72	SMART	SM00422	merrmega3
2	72	InterPro	IPR000551	MerR-type HTH domain
3	68	Pfam	PF13411	MerR HTH family regulatory protein
3	68	InterPro	IPR000551	MerR-type HTH domain
120	270	SMART	SM00871	AraC_E_bind_2
120	270	InterPro	IPR010499	Bacterial transcription activator, effector binding
1	123	FunFam	G3DSA:1.10.1660.10:FF:000016	MerR family transcriptional regulator

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

5 + 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 5XQL	X-ray	2.49 Å	A	100.0% 1-270	PDBe RCSB PDBj File	Viewing
PDB 5XBT	X-ray	2.50 Å	A,B	100.0% 1-270	PDBe RCSB PDBj File	Loaded
PDB 5YC9	X-ray	2.90 Å	A,B,C,D	100.0% 1-270	PDBe RCSB PDBj File	Loaded
PDB 5XBW	X-ray	3.11 Å	A,B,C,D	100.0% 1-270	PDBe RCSB PDBj File	Loaded
PDB 5XBI	X-ray	1.40 Å	A,B	55.9% 120-270	PDBe RCSB PDBj File	Loaded
AlphaFold PA4878	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				0.763

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.

65 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.

Ligand	Source crystal	MW · LogP · TPSA	Lipinski	PAINS	SMILES
81U	5XBI 1.40 Å Open crystal	211.2 Da LogP 2.07 TPSA 72.0	✓ Ro5	✓ Clean	`c1ccc2c(c1)nc3cc(c(cc3n2)O)N`
C2E	5XBT 2.50 Å Open crystal	690.4 Da LogP -3.05 TPSA 349.6	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@@](=O…`

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
118	6XL9	A0A8I3B050	430.2 Da LogP 3.06 TPSA 0.0	✓ Ro5	✓ Clean	`c1ccc(cc1)[Sb+](c2ccccc2)(c3ccccc3)c4ccccc4`
1N7	6XLK	A0A8I3B051	631.9 Da LogP 2.20 TPSA 164.4	2 viol.	✓ Clean	`C[C@H](CCC(=O)NCCC[N+](C)(C)CC(CS(=O)(=O)O)O)[C…`
ACH	3Q5S	P39075	146.2 Da LogP 0.26 TPSA 26.3	✓ Ro5	✓ Clean	`CC(=O)OCC[N+](C)(C)C`
BER	3D6Y	P39075	336.4 Da LogP 3.10 TPSA 40.8	✓ Ro5	✓ Clean	`COc1ccc2cc-3[n+](cc2c1OC)CCc4c3cc5c(c4)OCO5`
ET	3Q2Y	P39075	314.4 Da LogP 4.13 TPSA 55.9	✓ Ro5	Alert	`CC[n+]1c2cc(ccc2c3ccc(cc3c1c4ccccc4)N)N`
ETF	3D71	P39075	100.0 Da LogP 0.54 TPSA 20.2	✓ Ro5	✓ Clean	`C(C(F)(F)F)O`
FLC	3D71	P39075	189.1 Da LogP -5.25 TPSA 140.6	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O`
KAN	3Q5R	P39075	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@…`
M4A	3Q1M	P39075	158.2 Da LogP 2.13 TPSA 38.9	✓ Ro5	✓ Clean	`Cc1cc(c2ccccc2n1)N`
P4P	1EXJ	P39075	339.4 Da LogP 4.31 TPSA 0.0	✓ Ro5	✓ Clean	`c1ccc(cc1)[P+](c2ccccc2)(c3ccccc3)c4ccccc4`
PUY	3Q3D	P39075	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`CN(C)c1c2c(ncn1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H]…`
RHQ	3D6Z	P39075	443.6 Da LogP 4.43 TPSA 65.4	✓ Ro5	✓ Clean	`CCNc1cc2c(cc1C)C(=C3C=C(/C(=[NH+]\CC)/C=C3O2)C)…`
TAC	3Q5P	P39075	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`C[C@]1(c2cccc(c2C(=O)C3=C([C@]4([C@@H](C[C@@H]3…`

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
ZINC11525121	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C…`
ZINC119632	1.000	314.4 Da LogP 4.13 TPSA 55.9	✓ Ro5	Alert	`CC[n+]1c(-c2ccccc2)c2cc(N)ccc2c2ccc(N)cc21`
ZINC12501894	1.000	345.2 Da LogP -1.52 TPSA 174.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H]3CO[P@](=O)(O)O[C@@H]…`
ZINC17654095	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@…`
ZINC18202167	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3…`
ZINC1857793042	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC20410403	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3…`
ZINC21984166	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3…`
ZINC239173596	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C…`
ZINC239203289	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@@H]3…`
ZINC239203290	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@@H]3…`
ZINC239203291	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@@H]3…`
ZINC239203292	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@@H]3…`
ZINC242649355	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC242649358	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC242649360	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC242649362	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC245224172	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC245224173	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC245224174	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC245224175	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC33494013	1.000	345.2 Da LogP -1.52 TPSA 174.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H]3CO[P@](=O)(O)O[C@@H]…`
ZINC3779067	1.000	336.4 Da LogP 3.10 TPSA 40.8	✓ Ro5	✓ Clean	`COc1ccc2cc3[n+](cc2c1OC)CCc1cc2c(cc1-3)OCO2`
ZINC4095501	1.000	345.2 Da LogP -1.52 TPSA 174.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H]3CO[P@](=O)(O)O[C@H]3…`
ZINC4215819	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3C…`
ZINC43470138	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@H]1O[C@@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H…`
ZINC43771554	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C…`
ZINC4807269	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3…`
ZINC53147178	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@@H]2[C@@H](CO)O[C@@H…`
ZINC53147179	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@@H]2[C@@H](CO)O[C@@H]…`
ZINC5422104	1.000	211.2 Da LogP 2.07 TPSA 72.0	✓ Ro5	✓ Clean	`Nc1cc2nc3ccccc3nc2cc1O`
ZINC575338663	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C(…`
ZINC58994963	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@@H]2[C@H](CO)O[C@@H]…`
ZINC59065899	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@@H]2[C@H](O)[C@@H](n…`
ZINC59817042	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@@H]2[C@H](CO)O[C@H](…`
ZINC59817043	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@H]2[C@H](O)[C@@H](n3…`
ZINC59817045	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@H]2[C@H](O)[C@H](n3c…`
ZINC61389312	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@@H]2[C@@H](CO)O[C@H](…`
ZINC71789712	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@@H]2[C@@H](CO)O[C@H]…`
ZINC73333309	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@@H]2[C@H](CO)O[C@@H](…`
ZINC73333313	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@H]2[C@H](O)[C@@H](n3c…`
ZINC73333316	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@H]2[C@H](O)[C@H](n3cn…`
ZINC8101132	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@H]3O…`
ZINC8101133	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@H]3O…`
ZINC8101134	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@H](O[C@H]3O[…`
ZINC8101135	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@H](O[C@H]3O[…`
ZINC8214590	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC8217403	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC84441937	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3…`
ZINC88465990	1.000	345.2 Da LogP -1.52 TPSA 174.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H]3CO[P@@](=O)(O)O[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.