Protein profile

PA0376

RNA polymerase sigma factor RpoH

Genome: NC_002516.2

Gene: PA0376 rpoH Structure source: AlphaFold UniProt P42378

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Amino acids 284

Annotations 7

Features 34

PDB binders 9

Druggability 0.928

Overview

Basic information about this protein and its source genome.

Accession: PA0376
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA0376 rpoH
Status: annotated
Amino acids: 284
Structure source: AlphaFold

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0016987 Sigma factors act as the promoter specificity subunit of eubacterial and plant plastid multisubunit RNA polymerases, whose core subunit composition is often described as alpha(2)-beta-beta-prime. Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, the sigma factor binds specifically to promoter elements. The sigma subunit is released once elongation begins. GO:0006352 The initial step of transcription, consisting of the assembly of the RNA polymerase preinitiation complex (PIC) at a gene promoter, as well as the formation of the first few bonds of the RNA transcript. Transcription initiation includes abortive initiation events, which occur when the first few nucleotides are repeatedly synthesized and then released, and ends when promoter clearance takes place. GO:0009408 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 heat stimulus, a temperature stimulus above the optimal temperature for that organism. 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.

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 0.928

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0016987 Sigma factors act as the promoter specificity subunit of eubacterial and plant plastid multisubunit RNA polymerases, whose core subunit composition is often described as alpha(2)-beta-beta-prime. Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, the sigma factor binds specifically to promoter elements. The sigma subunit is released once elongation begins.
GO:0006352 The initial step of transcription, consisting of the assembly of the RNA polymerase preinitiation complex (PIC) at a gene promoter, as well as the formation of the first few bonds of the RNA transcript. Transcription initiation includes abortive initiation events, which occur when the first few nucleotides are repeatedly synthesized and then released, and ends when promoter clearance takes place.
GO:0009408 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 heat stimulus, a temperature stimulus above the optimal temperature for that organism.
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: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.

34 records

Show feature table

Start	End	DB	Term	Name
78	91	ProSitePatterns	PS00715	Sigma-70 factors family signature 1.
78	91	InterPro	IPR000943	RNA polymerase sigma-70
211	282	Gene3D	G3DSA:1.10.10.10	-
211	282	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily
253	273	Coils	Coil	Coil
15	123	FunFam	G3DSA:1.20.120.1810:FF:000001	RNA polymerase sigma factor RpoH
252	267	PRINTS	PR00046	Major sigma-70 factor signature
252	267	InterPro	IPR000943	RNA polymerase sigma-70
267	278	PRINTS	PR00046	Major sigma-70 factor signature
267	278	InterPro	IPR000943	RNA polymerase sigma-70
78	91	PRINTS	PR00046	Major sigma-70 factor signature
233	245	PRINTS	PR00046	Major sigma-70 factor signature
233	245	InterPro	IPR000943	RNA polymerase sigma-70
16	282	NCBIfam	TIGR02392	RNA polymerase sigma factor RpoH
16	282	InterPro	IPR012759	RNA polymerase sigma factor RpoH, proteobacteria
229	279	Pfam	PF04545	Sigma-70, region 4
229	279	InterPro	IPR007630	RNA polymerase sigma-70 region 4
55	123	Pfam	PF04542	Sigma-70 region 2
55	123	InterPro	IPR007627	RNA polymerase sigma-70 region 2
49	280	NCBIfam	TIGR02937	sigma-70 family RNA polymerase sigma factor
49	280	InterPro	IPR014284	RNA polymerase sigma-70 like domain
213	282	FunFam	G3DSA:1.10.10.10:FF:000285	RNA polymerase sigma factor RpoH
7	282	PANTHER	PTHR30376	SIGMA FACTOR RPOH HEAT SHOCK RELATED
15	123	SUPERFAMILY	SSF88946	Sigma2 domain of RNA polymerase sigma factors
15	123	InterPro	IPR013325	RNA polymerase sigma factor, region 2
16	123	Gene3D	G3DSA:1.20.120.1810	-
17	41	Pfam	PF00140	Sigma-70 factor, region 1.2
17	41	InterPro	IPR009042	RNA polymerase sigma-70 region 1.2
197	282	SUPERFAMILY	SSF88659	Sigma3 and sigma4 domains of RNA polymerase sigma factors
197	282	InterPro	IPR013324	RNA polymerase sigma factor, region 3/4-like
2	284	Hamap	MF_00961	RNA polymerase sigma factor RpoH [rpoH].
2	284	InterPro	IPR012759	RNA polymerase sigma factor RpoH, proteobacteria
252	278	ProSitePatterns	PS00716	Sigma-70 factors family signature 2.
252	278	InterPro	IPR000943	RNA polymerase sigma-70

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

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA0376	AlphaFold	—	—	full sequence	—	Viewing

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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				0.928
1				0.713
8				0.517

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.

59 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
118	6XL9	P00579	430.2 Da LogP 3.06 TPSA 0.0	✓ Ro5	✓ Clean	`c1ccc(cc1)[Sb+](c2ccccc2)(c3ccccc3)c4ccccc4`
1N7	6N57	P00579	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…`
1RL	4KN4	P00579	900.0 Da LogP 6.67 TPSA 216.4	3 viol.	✓ Clean	`CCN(CC)CCOc1cccc2c1N=C3c4c5c(c(c6c4C(=O)[C@](O6…`
1RM	4KN7	P00579	1035.2 Da LogP 6.62 TPSA 237.5	3 viol.	✓ Clean	`Cc1c(c2c3c4c1O[C@@](C4=O)(O/C=C/[C@@H]([C@H]([C…`
88G	5UHG	P9WGI1	358.4 Da LogP 3.97 TPSA 58.2	✓ Ro5	✓ Clean	`Cc1ccccc1NC(=O)[C@@H](Cc2ccccc2)NC(=O)c3ccccc3`
FI8	6BZO	P9WGI1	1058.1 Da LogP 6.23 TPSA 266.7	4 viol.	✓ Clean	`CCc1c(c(c(c(c1Cl)O)Cl)O)C(=O)O[C@@H]2[C@H](O[C@…`
KNG	6CUX	P00579	986.1 Da LogP 5.64 TPSA 292.6	4 viol.	Alert	`Cc1c(c2c3c(cc(c2O)NC(=O)/C(=C\CC[C@@H]([C@@H]([…`
RFP	5UH6	P9WGI1	823.0 Da LogP 4.34 TPSA 220.1	3 viol.	Alert	`Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C…`
SRN	6VVX	P9WGI1	807.0 Da LogP 6.80 TPSA 161.2	2 viol.	✓ Clean	`C[C@H]1[C@H]2C\C=C\[C@H]3[C@@H]([C@H]4C[C@@H](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
ZINC2852913	1.000	358.4 Da LogP 3.97 TPSA 58.2	✓ Ro5	✓ Clean	`Cc1ccccc1NC(=O)[C@@H](Cc1ccccc1)NC(=O)c1ccccc1`
ZINC2852914	1.000	358.4 Da LogP 3.97 TPSA 58.2	✓ Ro5	✓ Clean	`Cc1ccccc1NC(=O)[C@H](Cc1ccccc1)NC(=O)c1ccccc1`
ZINC1600536	0.762	296.4 Da LogP 2.68 TPSA 58.2	✓ Ro5	✓ Clean	`CC(=O)N[C@H](Cc1ccccc1)C(=O)Nc1ccccc1C`
ZINC6491543	0.762	296.4 Da LogP 2.68 TPSA 58.2	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](Cc1ccccc1)C(=O)Nc1ccccc1C`
ZINC2651112	0.723	364.5 Da LogP 4.04 TPSA 58.2	✓ Ro5	✓ Clean	`Cc1ccccc1NC(=O)[C@H](Cc1ccccc1)NC(=O)c1cccs1`
ZINC6650165	0.696	412.4 Da LogP 4.69 TPSA 58.2	✓ Ro5	✓ Clean	`O=C(N[C@@H](Cc1ccccc1)C(=O)Nc1ccccc1C(F)(F)F)c1…`
ZINC6650169	0.696	412.4 Da LogP 4.69 TPSA 58.2	✓ Ro5	✓ Clean	`O=C(N[C@H](Cc1ccccc1)C(=O)Nc1ccccc1C(F)(F)F)c1c…`
ZINC72399572	0.692	492.7 Da LogP 3.43 TPSA 93.0	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCCCN(C)C)[C@H]1CC[C@H]2[C@H]3[C@…`
ZINC1601274	0.690	344.4 Da LogP 3.67 TPSA 58.2	✓ Ro5	✓ Clean	`O=C(N[C@@H](Cc1ccccc1)C(=O)Nc1ccccc1)c1ccccc1`
ZINC6575235	0.690	344.4 Da LogP 3.67 TPSA 58.2	✓ Ro5	✓ Clean	`O=C(N[C@H](Cc1ccccc1)C(=O)Nc1ccccc1)c1ccccc1`
ZINC1157590	0.689	358.4 Da LogP 3.97 TPSA 58.2	✓ Ro5	✓ Clean	`Cc1ccc(NC(=O)[C@@H](Cc2ccccc2)NC(=O)c2ccccc2)cc1`
ZINC1157591	0.689	358.4 Da LogP 3.97 TPSA 58.2	✓ Ro5	✓ Clean	`Cc1ccc(NC(=O)[C@H](Cc2ccccc2)NC(=O)c2ccccc2)cc1`
ZINC1889002139	0.684	449.7 Da LogP 3.89 TPSA 89.8	✓ Ro5	✓ Clean	`CCCNC(=O)CC[C@@H](C)[C@H]1CC[C@@H]2[C@H]3[C@H](…`
ZINC1889002140	0.684	449.7 Da LogP 3.89 TPSA 89.8	✓ Ro5	✓ Clean	`CCCNC(=O)CC[C@@H](C)[C@H]1CC[C@@H]2[C@H]3[C@H](…`
ZINC1889002141	0.684	449.7 Da LogP 3.89 TPSA 89.8	✓ Ro5	✓ Clean	`CCCNC(=O)CC[C@@H](C)[C@H]1CC[C@@H]2[C@@H]3[C@H]…`
ZINC1889002142	0.684	449.7 Da LogP 3.89 TPSA 89.8	✓ Ro5	✓ Clean	`CCCNC(=O)CC[C@@H](C)[C@H]1CC[C@@H]2[C@@H]3[C@H]…`
ZINC11571738	0.660	427.5 Da LogP 4.58 TPSA 61.4	✓ Ro5	Alert	`Cc1cc(N2CCCC2)ccc1NC(=O)[C@@H](Cc1ccccc1)NC(=O)…`
ZINC11571742	0.660	427.5 Da LogP 4.58 TPSA 61.4	✓ Ro5	Alert	`Cc1cc(N2CCCC2)ccc1NC(=O)[C@H](Cc1ccccc1)NC(=O)c…`
ZINC22067099	0.660	373.5 Da LogP 4.08 TPSA 55.4	✓ Ro5	✓ Clean	`Cc1ccccc1COC(=O)[C@@H](Cc1ccccc1)NC(=O)c1ccccc1`
ZINC22067102	0.660	373.5 Da LogP 4.08 TPSA 55.4	✓ Ro5	✓ Clean	`Cc1ccccc1COC(=O)[C@H](Cc1ccccc1)NC(=O)c1ccccc1`
ZINC543330	0.659	298.3 Da LogP 2.81 TPSA 78.4	✓ Ro5	✓ Clean	`Cc1ccccc1NC(=O)N[C@@H](Cc1ccccc1)C(=O)O`
ZINC10022380	0.653	429.5 Da LogP 3.40 TPSA 87.3	✓ Ro5	✓ Clean	`Cc1cccc(C)c1NC(=O)CNC(=O)[C@@H](Cc1ccccc1)NC(=O…`
ZINC10022381	0.653	429.5 Da LogP 3.40 TPSA 87.3	✓ Ro5	✓ Clean	`Cc1cccc(C)c1NC(=O)CNC(=O)[C@H](Cc1ccccc1)NC(=O)…`
ZINC20399024	0.651	282.3 Da LogP 2.75 TPSA 58.2	✓ Ro5	✓ Clean	`Cc1ccccc1NC(=O)[C@@H](C)NC(=O)c1ccccc1`
ZINC20399026	0.651	282.3 Da LogP 2.75 TPSA 58.2	✓ Ro5	✓ Clean	`Cc1ccccc1NC(=O)[C@H](C)NC(=O)c1ccccc1`
ZINC5392338	0.651	310.4 Da LogP 2.55 TPSA 58.2	✓ Ro5	✓ Clean	`CC(C)NC(=O)[C@@H](Cc1ccccc1)NC(=O)c1ccccc1`
ZINC5392339	0.651	310.4 Da LogP 2.55 TPSA 58.2	✓ Ro5	✓ Clean	`CC(C)NC(=O)[C@H](Cc1ccccc1)NC(=O)c1ccccc1`
ZINC1127724	0.643	372.5 Da LogP 4.74 TPSA 58.2	✓ Ro5	✓ Clean	`Cc1ccccc1NC(=O)C(Cc1ccccc1)C(=O)Nc1ccccc1C`
ZINC118912648	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@@H](CCC(=O)NCC(=O)O)[C@H]1CC[C@H]2[C@H]3[C@…`
ZINC118912649	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@H]1CC[C@H]2[C@H]3[C@H…`
ZINC118912650	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@@H](CCC(=O)NCC(=O)O)[C@H]1CC[C@H]2[C@H]3[C@…`
ZINC118913700	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@@H](CCC(=O)NCC(=O)O)[C@H]1CC[C@H]2[C@@H]3[C…`
ZINC118913701	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@H]1CC[C@H]2[C@@H]3[C@…`
ZINC2060999620	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@H]1CC[C@H]2[C@@H]3[C@…`
ZINC2060999622	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@H]1CC[C@H]2[C@@H]3[C@…`
ZINC253497644	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@@H]1CC[C@@H]2[C@H]3[C…`
ZINC253497645	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@@H]1CC[C@@H]2[C@H]3[C…`
ZINC253497646	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@@H](CCC(=O)NCC(=O)O)[C@@H]1CC[C@@H]2[C@H]3[…`
ZINC253497647	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@@H](CCC(=O)NCC(=O)O)[C@@H]1CC[C@@H]2[C@H]3[…`
ZINC253608430	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@H]1CC[C@@H]2[C@@H]3[C…`
ZINC253615012	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@@H]1CC[C@@H]2[C@@H]3[…`
ZINC253615013	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@@H]1CC[C@@H]2[C@@H]3[…`
ZINC253615014	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@@H]1CC[C@@H]2[C@@H]3[…`
ZINC253615015	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@@H]1CC[C@@H]2[C@@H]3[…`
ZINC38144567	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@H]1CC[C@H]2[C@@H]3[C@…`
ZINC40164193	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@H]1CC[C@H]2[C@H]3[C@H…`
ZINC80852657	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@H]1CC[C@@H]2[C@H]3[C@…`
ZINC8143774	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@H]1CC[C@H]2[C@H]3[C@H…`
ZINC85426221	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@H]1CC[C@@H]2[C@@H]3[C…`
ZINC85426225	0.641	465.6 Da LogP 2.56 TPSA 127.1	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@H]1CC[C@@H]2[C@H]3[C@…`

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.