Protein profile

PA5239

transcription termination factor Rho

Genome: NC_002516.2

Gene: PA5239 rho Structure source: AlphaFold UniProt Q9HTV1

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Amino acids 419

Annotations 10

Features 36

PDB binders 11

Druggability 0.477

Overview

Basic information about this protein and its source genome.

Accession: PA5239
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA5239 rho
Status: annotated
Amino acids: 419
Structure source: AlphaFold

3.6.4.-

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0008186 Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of RNA, and it drives another reaction. GO:0004386 Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix. GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0003723 Binding to an RNA molecule or a portion thereof.

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 0.477

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

3.6.4.-

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:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0008186 Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of RNA, and it drives another reaction.
GO:0004386 Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
GO:0003723 Binding to an RNA molecule or a portion thereof.
GO:0006353 The completion of transcription: the RNA polymerase pauses, the RNA-DNA hybrid dissociates, followed by the release of the RNA polymerase from its DNA template.
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:0003676 Binding to a nucleic acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

36 records

Show feature table

Start	End	DB	Term	Name
2	417	NCBIfam	TIGR00767	transcription termination factor Rho
2	417	InterPro	IPR004665	Transcription termination factor Rho
160	363	Pfam	PF00006	ATP synthase alpha/beta family, nucleotide-binding domain
160	363	InterPro	IPR000194	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain
48	122	Gene3D	G3DSA:2.40.50.140	-
48	122	InterPro	IPR012340	Nucleic acid-binding, OB-fold
130	419	FunFam	G3DSA:3.40.50.300:FF:000072	Transcription termination factor Rho
1	419	Hamap	MF_01884	Transcription termination factor Rho [rho].
1	419	InterPro	IPR004665	Transcription termination factor Rho
48	123	ProSiteProfiles	PS51856	Rho RNA-binding domain profile.
48	123	InterPro	IPR011113	Rho termination factor, RNA-binding domain
130	419	Gene3D	G3DSA:3.40.50.300	-
130	419	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
1	46	SUPERFAMILY	SSF68912	Rho N-terminal domain-like
1	46	InterPro	IPR036269	Rho termination factor, N-terminal domain superfamily
90	371	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
90	371	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
48	122	FunFam	G3DSA:2.40.50.140:FF:000010	Transcription termination factor Rho
5	47	SMART	SM00959	Rho_N_2_a
5	47	InterPro	IPR011112	Rho termination factor, N-terminal
170	355	SMART	SM00382	AAA_5
170	355	InterPro	IPR003593	AAA+ ATPase domain
49	125	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
49	125	InterPro	IPR012340	Nucleic acid-binding, OB-fold
156	404	CDD	cd01128	rho_factor_C
156	404	InterPro	IPR041703	Transcription termination factor Rho, ATP binding domain
5	47	Pfam	PF07498	Rho termination factor, N-terminal domain
51	118	CDD	cd04459	Rho_CSD
51	118	InterPro	IPR011113	Rho termination factor, RNA-binding domain
52	118	SMART	SM00357	csp_8
52	118	InterPro	IPR011129	Cold shock domain
1	418	PANTHER	PTHR46425	TRANSCRIPTION TERMINATION FACTOR RHO
1	418	InterPro	IPR004665	Transcription termination factor Rho
1	47	Gene3D	G3DSA:1.10.720.10	-
52	125	Pfam	PF07497	Rho termination factor, RNA-binding domain
52	125	InterPro	IPR011113	Rho termination factor, RNA-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.

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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 PA5239	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
2				0.477
6				0.331
1				0.264
5				0.208

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.

61 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
AF3	6NJO	B7UMA6	84.0 Da LogP 0.88 TPSA 0.0	✓ Ro5	✓ Clean	`F[Al](F)F`
AGS	6SDX	P0A1B9	523.2 Da LogP -1.51 TPSA 262.1	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
ANP	5YBI	P0A1C1	506.2 Da LogP -2.06 TPSA 281.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
BCM	1XPO	P0AG30	302.3 Da LogP -3.30 TPSA 148.3	1 viol.	✓ Clean	`C[C@](CO)([C@@H]([C@@]12C(=O)N[C@@](C(=C)CCO1)(…`
BEF	3ICE	P0AG30	66.0 Da LogP 0.88 TPSA 0.0	✓ Ro5	✓ Clean	`[Be-](F)(F)F`
DG	6Z9R	P0AG30	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…`
DT	6Z9T	P0AG30	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O…`
FB	1XPR	P0AG30	330.3 Da LogP -3.73 TPSA 165.4	1 viol.	✓ Clean	`C[C@](CO)([C@@H]([C@@]12C(=O)N[C@@](C(=CC=O)CCO…`
FPD	1XPU	P0AG30	440.5 Da LogP -1.64 TPSA 165.4	1 viol.	✓ Clean	`C[C@](CO)([C@@H]([C@@]12C(=O)N[C@@]([C@@H](CCO1…`
IUM	3L0O	P38527	270.0 Da LogP -2.38 TPSA 46.1	✓ Ro5	✓ Clean	`[O-][U+4][O-]`
SPD	3ICE	P0AG30	145.2 Da LogP -0.34 TPSA 64.1	✓ Ro5	✓ Clean	`C(CCNCCCN)CN`

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)…`
ZINC13523519	1.000	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@@H](COP(=O)(O)O)O2)c(…`
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)…`
ZINC1481737	1.000	302.3 Da LogP -3.30 TPSA 148.3	1 viol.	✓ Clean	`C=C1CCO[C@]2([C@@H](O)[C@@](C)(O)CO)NC(=O)[C@@]…`
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)…`
ZINC1532628	1.000	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c(=…`
ZINC1678872	1.000	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c(=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…`
ZINC2047010	1.000	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c(=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…`
ZINC3870253	1.000	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(=O…`
ZINC3870254	1.000	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(=O)…`
ZINC4099038	1.000	302.3 Da LogP -3.30 TPSA 148.3	1 viol.	✓ Clean	`C=C1CCO[C@]2([C@@H](O)[C@](C)(O)CO)NC(=O)[C@@]1…`
ZINC4099039	1.000	302.3 Da LogP -3.30 TPSA 148.3	1 viol.	✓ Clean	`C=C1CCO[C@]2([C@H](O)[C@](C)(O)CO)NC(=O)[C@@]1(…`
ZINC4099040	1.000	302.3 Da LogP -3.30 TPSA 148.3	1 viol.	✓ Clean	`C=C1CCO[C@]2([C@H](O)[C@@](C)(O)CO)NC(=O)[C@@]1…`
ZINC6523446	1.000	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c(=…`
ZINC967753	1.000	302.3 Da LogP -3.30 TPSA 148.3	1 viol.	✓ Clean	`C=C1CCO[C@@]2([C@H](O)[C@](C)(O)CO)NC(=O)[C@]1(…`
ZINC967754	1.000	302.3 Da LogP -3.30 TPSA 148.3	1 viol.	✓ Clean	`C=C1CCO[C@@]2([C@H](O)[C@@](C)(O)CO)NC(=O)[C@]1…`
ZINC27564039	0.933	202.3 Da LogP -0.36 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCCNCCCNCCCN`
ZINC13377742	0.929	230.4 Da LogP 0.42 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCCNCCCCNCCCCN`
ZINC1532734	0.929	202.3 Da LogP -0.36 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCNCCCCNCCCN`
ZINC1598087	0.867	215.4 Da LogP 1.61 TPSA 64.1	✓ Ro5	✓ Clean	`NCCCCCCNCCCCCCN`
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…`
ZINC12360002	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12360703	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12503599	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC16546165	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…`
ZINC31977053	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC4806433	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC53683898	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC8586020	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC8586022	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC12503053	0.837	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC33979243	0.837	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC33979244	0.837	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)OP(=O)…`
ZINC33979245	0.837	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)OP(=…`
ZINC33979246	0.837	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC8215882	0.837	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC17107637	0.833	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@@H](COP(N)(N)=O)O2)c(…`
ZINC17107641	0.833	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](COP(N)(N)=O)O2)c(=…`
ZINC5493427	0.833	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](COP(N)(N)=O)O2)c(=O…`
ZINC5493430	0.833	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](COP(N)(N)=O)O2)c(=…`
ZINC13507072	0.804	482.2 Da LogP -1.16 TPSA 244.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)O[P@…`
ZINC33979251	0.804	482.2 Da LogP -1.16 TPSA 244.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)O[P@@…`

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.