Protein profile

PA0527

transcriptional regulator Dnr

Genome: NC_002516.2

Gene: dnr PA0527 PACL_0281 Structure source: Experimental + AlphaFold UniProt G3XCW6 UniProt Q51441

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Amino acids 227

Annotations 9

Features 23

PDB binders 7

Druggability 0.872

Overview

Basic information about this protein and its source genome.

Accession: PA0527
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: dnr PA0527 PACL_0281
Status: annotated
Amino acids: 227
Structure source: Experimental + AlphaFold

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. 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: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:0045893 Any process that activates or increases 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 0.872

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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
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: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:0045893 Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
GO:0071731 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus.
GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records

Show feature table

Start	End	DB	Term	Name
171	219	SMART	SM00419	crpmeuga4
171	219	InterPro	IPR012318	Crp-type HTH domain
156	224	Pfam	PF13545	Crp-like helix-turn-helix domain
156	224	InterPro	IPR012318	Crp-type HTH domain
16	123	CDD	cd00038	CAP_ED
16	123	InterPro	IPR000595	Cyclic nucleotide-binding domain
150	227	Gene3D	G3DSA:1.10.10.10	-
150	227	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily
150	224	SUPERFAMILY	SSF46785	Winged helix DNA-binding domain
150	224	InterPro	IPR036390	Winged helix DNA-binding domain superfamily
1	149	Gene3D	G3DSA:2.60.120.10	Jelly Rolls
1	149	InterPro	IPR014710	RmlC-like jelly roll fold
9	150	SUPERFAMILY	SSF51206	cAMP-binding domain-like
9	150	InterPro	IPR018490	Cyclic nucleotide-binding domain superfamily
8	226	PANTHER	PTHR24567	CRP FAMILY TRANSCRIPTIONAL REGULATORY PROTEIN
16	137	ProSiteProfiles	PS50042	cAMP/cGMP binding motif profile.
16	137	InterPro	IPR000595	Cyclic nucleotide-binding domain
151	221	ProSiteProfiles	PS51063	Crp-type HTH domain profile.
151	221	InterPro	IPR012318	Crp-type HTH domain
16	135	SMART	SM00100	cnmp_10
16	135	InterPro	IPR000595	Cyclic nucleotide-binding domain
35	122	Pfam	PF00027	Cyclic nucleotide-binding domain
35	122	InterPro	IPR000595	Cyclic nucleotide-binding domain

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

2 + 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 3DKW	X-ray	3.60 Å	A,B,C,D,E,F,G,H,I,J	100.0% 1-227	PDBe RCSB PDBj File	Viewing
PDB 2Z69	X-ray	2.10 Å	A,B,C	66.5% 1-151	PDBe RCSB PDBj File	Loaded
AlphaFold PA0527	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
2				0.701
1				0.617

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.

57 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
2FT	3LA3	P0A4U6	168.1 Da LogP 0.57 TPSA 74.6	✓ Ro5	✓ Clean	`C(CC(C(=O)O)(F)F)C(=O)O`
AKG	3LA2	P0A4U6	146.1 Da LogP -0.50 TPSA 91.7	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)C(=O)O`
BTB	2XGX	P29283	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`C(CO)N(CCO)C(CO)(CO)CO`
N6R	3I59	P9WMH3	447.4 Da LogP 1.64 TPSA 140.8	✓ Ro5	✓ Clean	`C[C@H](Cc1ccccc1)Nc2c3c(ncn2)n(cn3)[C@H]4[C@@H]…`
N6S	3I59	P9WMH3	447.4 Da LogP 1.64 TPSA 140.8	✓ Ro5	✓ Clean	`C[C@@H](Cc1ccccc1)Nc2c3c(ncn2)n(cn3)[C@H]4[C@@H…`
PCG	4N9I	C3SQJ7	345.2 Da LogP -1.52 TPSA 174.8	✓ Ro5	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@H]4C(O3)CO[P@](=O)(O4)…`
SP1	4R8H	P0ACJ8	345.3 Da LogP -0.70 TPSA 137.8	✓ Ro5	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)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
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]…`
ZINC1615342	1.000	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`OCCN(CCO)C(CO)(CO)CO`
ZINC31474923	0.761	419.3 Da LogP 1.21 TPSA 140.8	✓ Ro5	✓ Clean	`O=[P@@]1(O)OC[C@H]2O[C@@H](n3cnc4c(NCc5ccccc5)n…`
ZINC13829346	0.689	433.3 Da LogP 0.85 TPSA 157.9	✓ Ro5	✓ Clean	`O=C(Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@@](=O)(O)…`
ZINC44559643	0.689	433.3 Da LogP 0.85 TPSA 157.9	✓ Ro5	✓ Clean	`O=C(Nc1ncnc2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C…`
ZINC13516498	0.662	399.3 Da LogP 0.34 TPSA 157.9	✓ Ro5	✓ Clean	`CCCC(=O)Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)…`
ZINC14948944	0.662	399.3 Da LogP 0.34 TPSA 157.9	✓ Ro5	✓ Clean	`CCCC(=O)Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)…`
ZINC256769854	0.662	399.3 Da LogP 0.34 TPSA 157.9	✓ Ro5	✓ Clean	`CCCC(=O)Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)…`
ZINC256769855	0.662	399.3 Da LogP 0.34 TPSA 157.9	✓ Ro5	✓ Clean	`CCCC(=O)Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)…`
ZINC12502230	0.606	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O[C@@…`
ZINC3581269	0.606	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O[C@H…`
ZINC3869448	0.606	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C@@H]…`
ZINC3869449	0.606	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H]2CO[P@](=O)(O)O[C@@H…`
ZINC3869450	0.606	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C@@H]…`
ZINC3869451	0.606	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H]2CO[P@](=O)(O)O[C@@H…`
ZINC3873977	0.606	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O[C@H…`
ZINC4245698	0.606	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O[C@@…`
ZINC34206393	0.538	285.2 Da LogP -1.71 TPSA 139.3	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](O)[C@H]2F)c…`
ZINC3783111	0.538	285.2 Da LogP -1.71 TPSA 139.3	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2F)…`
ZINC3797144	0.538	285.2 Da LogP -1.71 TPSA 139.3	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2F)c…`
ZINC3950	0.538	285.2 Da LogP -1.71 TPSA 139.3	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@H](O)[C@H]2F)c(…`
ZINC5848	0.538	285.2 Da LogP -1.71 TPSA 139.3	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@H](O)[C@@H]2F)c…`
ZINC6119309	0.538	285.2 Da LogP -1.71 TPSA 139.3	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@H](CO)[C@@H](O)[C@@H]2F)c…`
ZINC6585361	0.538	285.2 Da LogP -1.71 TPSA 139.3	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@H](O)[C@H]2F)c(…`
ZINC66155299	0.538	285.2 Da LogP -1.71 TPSA 139.3	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@H](O)[C@@H]2F)c…`
ZINC1616450	0.536	254.3 Da LogP -1.28 TPSA 82.3	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)[C@@H]1CCCN1)[C@@H]1CCCN1`
ZINC5600257	0.536	254.3 Da LogP -1.28 TPSA 82.3	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)[C@H]1CCCN1)[C@H]1CCCN1`
ZINC8655607	0.536	254.3 Da LogP -1.28 TPSA 82.3	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)[C@H]1CCCN1)[C@@H]1CCCN1`
ZINC4095503	0.533	330.2 Da LogP -1.11 TPSA 148.8	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O…`
ZINC4533542	0.533	330.2 Da LogP -1.11 TPSA 148.8	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C…`
ZINC4533545	0.533	330.2 Da LogP -1.11 TPSA 148.8	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C…`
ZINC4899613	0.531	212.2 Da LogP -0.19 TPSA 69.6	✓ Ro5	✓ Clean	`O=C(O)[C@@H]1CCCN1C(=O)[C@@H]1CCCN1`
ZINC4974454	0.531	212.2 Da LogP -0.19 TPSA 69.6	✓ Ro5	✓ Clean	`O=C(O)[C@H]1CCCN1C(=O)[C@H]1CCCN1`
ZINC4974455	0.531	212.2 Da LogP -0.19 TPSA 69.6	✓ Ro5	✓ Clean	`O=C(O)[C@H]1CCCN1C(=O)[C@@H]1CCCN1`
ZINC4974456	0.531	212.2 Da LogP -0.19 TPSA 69.6	✓ Ro5	✓ Clean	`O=C(O)[C@@H]1CCCN1C(=O)[C@H]1CCCN1`
ZINC757216905	0.531	212.3 Da LogP 0.44 TPSA 61.4	✓ Ro5	✓ Clean	`O=C(O)[C@@H]1C[C@@H]([C@@H]2CCCNC2)CCN1`
ZINC757216906	0.531	212.3 Da LogP 0.44 TPSA 61.4	✓ Ro5	✓ Clean	`O=C(O)[C@@H]1C[C@H]([C@@H]2CCCNC2)CCN1`
ZINC757216908	0.531	212.3 Da LogP 0.44 TPSA 61.4	✓ Ro5	✓ Clean	`O=C(O)[C@@H]1C[C@@H]([C@H]2CCCNC2)CCN1`
ZINC757216910	0.531	212.3 Da LogP 0.44 TPSA 61.4	✓ Ro5	✓ Clean	`O=C(O)[C@@H]1C[C@H]([C@H]2CCCNC2)CCN1`
ZINC11616172	0.530	469.4 Da LogP 1.69 TPSA 164.0	1 viol.	✓ Clean	`CCCC(=O)Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)…`
ZINC13718644	0.530	469.4 Da LogP 1.69 TPSA 164.0	1 viol.	✓ Clean	`CCCC(=O)Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)…`
ZINC1529045110	0.530	469.4 Da LogP 1.69 TPSA 164.0	1 viol.	✓ Clean	`CCCC(=O)Nc1ncnc2c1ncn2[C@@H]1O[C@H]2CO[P@](=O)(…`
ZINC33998808	0.530	441.4 Da LogP 2.64 TPSA 129.8	✓ Ro5	✓ Clean	`CCCCNc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O…`
ZINC3861742	0.530	469.4 Da LogP 1.69 TPSA 164.0	1 viol.	✓ Clean	`CCCC(=O)Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)…`
ZINC3871786	0.530	469.4 Da LogP 1.69 TPSA 164.0	1 viol.	✓ Clean	`CCCC(=O)Nc1ncnc2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O…`
ZINC3871787	0.530	469.4 Da LogP 1.69 TPSA 164.0	1 viol.	✓ Clean	`CCCC(=O)Nc1ncnc2c1ncn2[C@@H]1O[C@H]2CO[P@](=O)(…`
ZINC3871788	0.530	469.4 Da LogP 1.69 TPSA 164.0	1 viol.	✓ Clean	`CCCC(=O)Nc1ncnc2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O…`
ZINC3871789	0.530	469.4 Da LogP 1.69 TPSA 164.0	1 viol.	✓ Clean	`CCCC(=O)Nc1ncnc2c1ncn2[C@@H]1O[C@H]2CO[P@](=O)(…`
ZINC4245601	0.530	469.4 Da LogP 1.69 TPSA 164.0	1 viol.	✓ Clean	`CCCC(=O)Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)…`
ZINC4257714	0.530	469.4 Da LogP 1.69 TPSA 164.0	1 viol.	✓ Clean	`CCCC(=O)Nc1ncnc2c1ncn2[C@@H]1O[C@H]2CO[P@](=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.