Target Pathogen

Overview

Basic information about this protein and its source genome.

Accession: PA5125
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: ntrC PA5125
Status: annotated
Amino acids: 476
Structure source: AlphaFold

GO

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0032993 A macromolecular complex containing both protein and DNA molecules. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0000987 Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site, located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by some RNA polymerase. Cis-regulatory sites are often referred to as a sequence motifs, enhancers, or silencers. GO:0001216 A DNA-binding transcription factor activity that activates or increases transcription of specific gene sets. GO:0000156 Responds to a phosphorelay sensor to initiate a change in cell state or activity. The activity of the response regulator is regulated by transfer of a phosphate from a histidine residue in the sensor, to an aspartate residue in the response regulator. Many but not all response regulators act as transcriptional regulators to elicit a response.

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 0.57

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

14 GO

Gene Ontology (GO)

14

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0032993 A macromolecular complex containing both protein and DNA molecules.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0000987 Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site, located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by some RNA polymerase. Cis-regulatory sites are often referred to as a sequence motifs, enhancers, or silencers.
GO:0001216 A DNA-binding transcription factor activity that activates or increases transcription of specific gene sets.
GO:0000156 Responds to a phosphorelay sensor to initiate a change in cell state or activity. The activity of the response regulator is regulated by transfer of a phosphate from a histidine residue in the sensor, to an aspartate residue in the response regulator. Many but not all response regulators act as transcriptional regulators to elicit a response.
GO:0045893 Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
GO:0006808 Any process that modulates the frequency, rate or extent of nitrogen utilization.
GO:0000160 A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
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).
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:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
GO:0008134 Binding to a transcription factor, a protein required to initiate or regulate transcription.

Sequence Features

Domain/signature hits from InterPro and related databases.

44 records

Show feature table

Start	End	DB	Term	Name
5	119	CDD	cd19919	REC_NtrC
2	133	Gene3D	G3DSA:3.40.50.2300	-
7	463	NCBIfam	TIGR01818	nitrogen regulation protein NR(I)
7	463	InterPro	IPR010114	DNA-binding transcriptional regulator NtrC
133	311	FunFam	G3DSA:3.40.50.300:FF:000006	DNA-binding transcriptional regulator NtrC
313	384	Gene3D	G3DSA:1.10.8.60	-
140	384	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
140	384	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
227	242	ProSitePatterns	PS00676	Sigma-54 interaction domain ATP-binding region B signature.
227	242	InterPro	IPR025943	Sigma-54 interaction domain, ATP-binding site 2
312	384	FunFam	G3DSA:1.10.8.60:FF:000014	DNA-binding transcriptional regulator NtrC
381	465	SUPERFAMILY	SSF46689	Homeodomain-like
381	465	InterPro	IPR009057	Homeobox-like domain superfamily
5	466	PANTHER	PTHR32071	TRANSCRIPTIONAL REGULATORY PROTEIN
2	131	FunFam	G3DSA:3.40.50.2300:FF:000018	DNA-binding transcriptional regulator NtrC
165	178	ProSitePatterns	PS00675	Sigma-54 interaction domain ATP-binding region A signature.
165	178	InterPro	IPR025662	Sigma-54 interaction domain, ATP-binding site 1
142	310	CDD	cd00009	AAA
446	466	PRINTS	PR01590	FIS bacterial regulatory protein HTH signature
446	466	InterPro	IPR002197	DNA binding HTH domain, Fis-type
429	446	PRINTS	PR01590	FIS bacterial regulatory protein HTH signature
429	446	InterPro	IPR002197	DNA binding HTH domain, Fis-type
385	466	Gene3D	G3DSA:1.10.10.60	-
7	115	Pfam	PF00072	Response regulator receiver domain
7	115	InterPro	IPR001789	Signal transduction response regulator, receiver domain
134	312	Gene3D	G3DSA:3.40.50.300	-
134	312	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
141	370	ProSiteProfiles	PS50045	Sigma-54 interaction domain profile.
141	370	InterPro	IPR002078	RNA polymerase sigma factor 54 interaction domain
423	463	Pfam	PF02954	Bacterial regulatory protein, Fis family
423	463	InterPro	IPR002197	DNA binding HTH domain, Fis-type
161	304	SMART	SM00382	AAA_5
161	304	InterPro	IPR003593	AAA+ ATPase domain
354	363	ProSitePatterns	PS00688	Sigma-54 interaction domain C-terminal part signature.
354	363	InterPro	IPR025944	Sigma-54 interaction domain, conserved site
5	116	SMART	SM00448	REC_2
5	116	InterPro	IPR001789	Signal transduction response regulator, receiver domain
6	120	ProSiteProfiles	PS50110	Response regulatory domain profile.
6	120	InterPro	IPR001789	Signal transduction response regulator, receiver domain
141	308	Pfam	PF00158	Sigma-54 interaction domain
141	308	InterPro	IPR002078	RNA polymerase sigma factor 54 interaction domain
5	186	SUPERFAMILY	SSF52172	CheY-like
5	186	InterPro	IPR011006	CheY-like superfamily
385	466	FunFam	G3DSA:1.10.10.60:FF:000088	DNA-binding transcriptional regulator NtrC

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 PA5125	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
12				0.57
1				0.309
3				0.269

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.

16 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
08T	4LZZ	O67198	—	—	—	`[Be](OP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@…`
5QT	5EP3	Q1ZS18	272.3 Da LogP 0.83 TPSA 99.9	✓ Ro5	✓ Clean	`CC(C)(C)COC(=O)CNC1=NNC(=O)NC1=S`
AZU	5EP2	Q1ZS18	273.3 Da LogP 0.14 TPSA 104.9	✓ Ro5	✓ Clean	`CC(C)(C)COC(=O)CSC1=NNC(=O)NC1=O`
BEF	1L5Y	P13632	66.0 Da LogP 0.88 TPSA 0.0	✓ Ro5	✓ Clean	`[Be-](F)(F)F`
BF2	1L5Y	P13632	47.0 Da LogP 0.46 TPSA 0.0	✓ Ro5	✓ Clean	`[Be](F)F`
BF4	1L5Y	P13632	85.0 Da LogP 1.30 TPSA 0.0	✓ Ro5	✓ Clean	`[Be-2](F)(F)(F)F`

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
ZINC115597	0.634	243.3 Da LogP 0.17 TPSA 95.7	✓ Ro5	✓ Clean	`CC(C)(C)C(=O)CSc1n[nH]c(=O)[nH]c1=O`
ZINC98045385	0.630	343.4 Da LogP 2.23 TPSA 104.9	✓ Ro5	✓ Clean	`CCCCCCCCCCOC(=O)CSc1n[nH]c(=O)[nH]c1=O`
ZINC1042130	0.556	214.2 Da LogP -1.57 TPSA 116.9	✓ Ro5	✓ Clean	`CCOC(=O)CNc1n[nH]c(=O)[nH]c1=O`
ZINC2472023	0.532	228.2 Da LogP -1.18 TPSA 116.9	✓ Ro5	✓ Clean	`CCCOC(=O)CNc1n[nH]c(=O)[nH]c1=O`
ZINC1232291	0.523	200.2 Da LogP -1.96 TPSA 116.9	✓ Ro5	✓ Clean	`COC(=O)CNc1n[nH]c(=O)[nH]c1=O`
ZINC2473652	0.521	242.2 Da LogP -0.93 TPSA 116.9	✓ Ro5	✓ Clean	`CC(C)COC(=O)CNc1n[nH]c(=O)[nH]c1=O`
ZINC1748584	0.511	245.3 Da LogP -0.50 TPSA 104.9	✓ Ro5	✓ Clean	`COC(=O)CCCSc1n[nH]c(=O)[nH]c1=O`
ZINC2461660	0.510	242.2 Da LogP -0.79 TPSA 116.9	✓ Ro5	✓ Clean	`CCCCOC(=O)CNc1n[nH]c(=O)[nH]c1=O`
ZINC1282722	0.510	334.4 Da LogP 1.49 TPSA 107.7	✓ Ro5	✓ Clean	`CC(C)(C)c1ccc(NC(=O)CSc2n[nH]c(=O)[nH]c2=O)cc1`
ZINC115606	0.500	277.3 Da LogP 0.74 TPSA 95.7	✓ Ro5	✓ Clean	`Cc1ccc(C(=O)CSc2n[nH]c(=O)[nH]c2=O)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.

PA5125