Protein profile

PA5380

protein GbdR

Genome: NC_002516.2

Gene: gbdR PA5380 Structure source: AlphaFold UniProt Q9HTI4

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Amino acids 367

Annotations 10

Features 23

PDB binders 2

Druggability 0.709

Overview

Basic information about this protein and its source genome.

Accession: PA5380
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: gbdR PA5380
Status: annotated
Amino acids: 367
Structure source: 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: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:0031457 The chemical reactions and pathways resulting in the breakdown of glycine betaine, N-trimethylglycine. GO:0045764 Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amino acid. GO:0009896 Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Gut microbiome off-target: hit
Essential (DEG): Y
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 0.709

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MTTYAPGVPPQNRNPQSIGFLLLDNFTLISLASAVEPLRMANQLSGRELYRWHTLSLDGRQVWASDGLQITPDAGTDNAPAVDCVIVCGGVGIQRSVTREHVTFLQAQARQGRRLGAVCTGSWALARAGLLDGYDCSVHWECLAAMQEAFPRVAMSTRLFSIDRNRFTSSGGTAPMDMMLHLIGREHGRELSAAISEMFIYERIRNEQDHQRVPLKHMLGTNQPKLQEIVALMEANLEEPIDLDELAVYVNVSRRQLERLFQKYLHCSPSRYYLKLRLIRARQLLKQTSMSIIEVASVCGFVSTPHFSKCYREYFGIPPRDERQGQPLGQPVVLMPIPQDLALMPNSSALSALSQAQGESTFASVRI

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

10 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: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:0031457 The chemical reactions and pathways resulting in the breakdown of glycine betaine, N-trimethylglycine.
GO:0045764 Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amino acid.
GO:0009896 Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances.
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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records

Show feature table

Start	End	DB	Term	Name
277	319	ProSitePatterns	PS00041	Bacterial regulatory proteins, araC family signature.
277	319	InterPro	IPR018062	HTH domain AraC-type, conserved site
20	183	Pfam	PF01965	DJ-1/PfpI family
20	183	InterPro	IPR002818	DJ-1/PfpI
224	274	SUPERFAMILY	SSF46689	Homeodomain-like
224	274	InterPro	IPR009057	Homeobox-like domain superfamily
227	325	ProSiteProfiles	PS01124	Bacterial regulatory proteins, araC family DNA-binding domain profile.
227	325	InterPro	IPR018060	DNA binding HTH domain, AraC-type
276	325	SUPERFAMILY	SSF46689	Homeodomain-like
276	325	InterPro	IPR009057	Homeobox-like domain superfamily
12	213	FunFam	G3DSA:3.40.50.880:FF:000061	AraC family transcriptional regulator
240	323	SMART	SM00342	aracneu4
240	323	InterPro	IPR018060	DNA binding HTH domain, AraC-type
18	202	CDD	cd03136	GATase1_AraC_ArgR_like
13	263	PANTHER	PTHR43130	ARAC-FAMILY TRANSCRIPTIONAL REGULATOR
220	325	FunFam	G3DSA:1.10.10.60:FF:000090	Transcriptional regulator ArgR, AraC family
15	205	SUPERFAMILY	SSF52317	Class I glutamine amidotransferase-like
15	205	InterPro	IPR029062	Class I glutamine amidotransferase-like
220	326	Gene3D	G3DSA:1.10.10.60	-
246	324	Pfam	PF12833	Helix-turn-helix domain
246	324	InterPro	IPR018060	DNA binding HTH domain, AraC-type
12	213	Gene3D	G3DSA:3.40.50.880	-
12	213	InterPro	IPR029062	Class I glutamine amidotransferase-like

3D Structure

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

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Structural evidence

0 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA5380	AlphaFold	—	—	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				0.279
2				0.215

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

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
NHE	3NOQ	Q4K977	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`C1CCC(CC1)NCCS(=O)(=O)O`
QCV	6UND	Q4K977	150.1 Da LogP 1.93 TPSA 55.5	✓ Ro5	✓ Clean	`C=Nc1ccc(cc1)N(=O)=O`

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
ZINC1710230	1.000	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC1CCCCC1`
ZINC2004372	0.786	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC1CCCCC1`
ZINC38364153	0.786	235.3 Da LogP 1.58 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC1CCCCC1`
ZINC1532902	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC100349549	0.667	272.2 Da LogP 3.92 TPSA 111.0	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/N=N\c2ccc([N+](=O)[O-])cc2)c…`
ZINC13477308	0.667	272.2 Da LogP 3.92 TPSA 111.0	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/N=N/c2ccc([N+](=O)[O-])cc2)c…`
ZINC3593496	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC14686440	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC104039967	0.615	288.2 Da LogP 3.43 TPSA 124.7	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(N=[N+]([O-])c2ccc([N+](=O)[O-…`
ZINC13398039	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC2528012	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC100172111	0.571	227.2 Da LogP 4.01 TPSA 67.9	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/N=N\c2ccccc2)cc1`
ZINC18084630	0.571	227.2 Da LogP 4.01 TPSA 67.9	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/N=N/c2ccccc2)cc1`
ZINC254365173	0.571	227.2 Da LogP 4.01 TPSA 67.9	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(N=Nc2ccccc2)cc1`
ZINC146315135	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@@](O)(CC(=O)O)C(=O)O`
ZINC146315336	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@](O)(CC(=O)O)C(=O)O`
ZINC19367005	0.560	224.4 Da LogP 2.83 TPSA 24.1	✓ Ro5	✓ Clean	`C1CCC(NCCNC2CCCCC2)CC1`
ZINC26468763	0.559	243.3 Da LogP -1.35 TPSA 100.5	✓ Ro5	✓ Clean	`O=S(=O)(O)CCN[C@@H]1CCS(=O)(=O)C1`
ZINC26468770	0.559	243.3 Da LogP -1.35 TPSA 100.5	✓ Ro5	✓ Clean	`O=S(=O)(O)CCN[C@H]1CCS(=O)(=O)C1`
ZINC1850353	0.556	206.1 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC(O)(CC(=O)O)CC(=O)O`
ZINC5188799	0.556	280.5 Da LogP 4.39 TPSA 24.1	✓ Ro5	✓ Clean	`C(CCCNC1CCCCC1)CCNC1CCCCC1`
ZINC100009138	0.552	243.2 Da LogP 3.72 TPSA 88.1	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/N=N\c2ccc(O)cc2)cc1`
ZINC100009140	0.552	243.2 Da LogP 3.72 TPSA 88.1	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/N=N/c2ccc(O)cc2)cc1`
ZINC12405069	0.552	242.2 Da LogP 3.59 TPSA 93.9	✓ Ro5	Alert	`Nc1ccc(N=Nc2ccc([N+](=O)[O-])cc2)cc1`
ZINC254392989	0.552	243.2 Da LogP 3.72 TPSA 88.1	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(N=Nc2ccc(O)cc2)cc1`
ZINC3861520	0.552	242.2 Da LogP 3.59 TPSA 93.9	✓ Ro5	Alert	`Nc1ccc(/N=N/c2ccc([N+](=O)[O-])cc2)cc1`
ZINC4461716	0.552	241.3 Da LogP 4.32 TPSA 67.9	✓ Ro5	Alert	`Cc1ccc(/N=N/c2ccc([N+](=O)[O-])cc2)cc1`
ZINC100838097	0.548	336.3 Da LogP 2.98 TPSA 145.1	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/N=N/S(=O)(=O)c2ccc([N+](=O)[…`
ZINC1604377	0.542	320.3 Da LogP 4.84 TPSA 86.3	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(-c2ccc(-c3ccc([N+](=O)[O-])cc…`
ZINC1648209	0.542	244.2 Da LogP 3.17 TPSA 86.3	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(-c2ccc([N+](=O)[O-])cc2)cc1`
ZINC100480229	0.533	271.2 Da LogP 3.25 TPSA 98.6	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(/C=N\c2ccc([N+](=O)[O-])cc2)c…`
ZINC12403614	0.533	271.2 Da LogP 3.25 TPSA 98.6	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(/C=N/c2ccc([N+](=O)[O-])cc2)c…`
ZINC254391581	0.533	271.2 Da LogP 3.25 TPSA 98.6	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(C=Nc2ccc([N+](=O)[O-])cc2)cc1`
ZINC39239102	0.533	214.2 Da LogP 1.95 TPSA 72.6	✓ Ro5	✓ Clean	`CS(C)(=O)=Nc1ccc([N+](=O)[O-])cc1`
ZINC2168583	0.529	237.3 Da LogP 0.16 TPSA 86.6	✓ Ro5	✓ Clean	`O=S(=O)(O)C[C@@H](O)CNC1CCCCC1`
ZINC2168584	0.529	237.3 Da LogP 0.16 TPSA 86.6	✓ Ro5	✓ Clean	`O=S(=O)(O)C[C@H](O)CNC1CCCCC1`
ZINC13398014	0.522	220.2 Da LogP -1.07 TPSA 110.1	✓ Ro5	✓ Clean	`COC(=O)CC(O)(CC(=O)OC)C(=O)O`
ZINC3861629	0.522	206.1 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C(O)(CC(=O)O)CC(=O)O`
ZINC130127586	0.515	260.4 Da LogP 1.38 TPSA 58.2	✓ Ro5	✓ Clean	`O=S(=O)(NCCNC1CCCCCC1)C1CC1`
ZINC78421079	0.515	210.3 Da LogP 1.43 TPSA 41.1	✓ Ro5	✓ Clean	`O=C(NCCNC1CCCCC1)C1CC1`
ZINC104075553	0.500	243.2 Da LogP 3.52 TPSA 81.6	✓ Ro5	Alert	`O=[N+]([O-])c1ccc([N+]([O-])=Nc2ccccc2)cc1`
ZINC1511626	0.500	249.0 Da LogP 2.20 TPSA 43.1	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(I)cc1`
ZINC165485	0.500	301.8 Da LogP 3.04 TPSA 46.2	✓ Ro5	✓ Clean	`O=S(=O)(CCNC1CCCCC1)c1ccc(Cl)cc1`
ZINC17005675	0.500	257.2 Da LogP 4.02 TPSA 77.1	✓ Ro5	Alert	`COc1ccc(/N=N/c2ccc([N+](=O)[O-])cc2)cc1`
ZINC4113982	0.500	270.3 Da LogP 4.08 TPSA 71.1	✓ Ro5	Alert	`CN(C)c1ccc(/N=N/c2ccc([N+](=O)[O-])cc2)cc1`
ZINC60934954	0.500	315.9 Da LogP 3.43 TPSA 46.2	✓ Ro5	✓ Clean	`O=S(=O)(CCNC1CCCCCC1)c1ccc(Cl)cc1`

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.