Protein profile

VK055_3643

alternative sigma factor RpoH

Genome: KpATCC43816

Gene: AIK82198.1 rpoH Structure source: AlphaFold + ColabFold UniProt A0A0H3H469

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Amino acids 257

Annotations 4

Features 35

PDB binders 9

Druggability 0.286

Overview

Basic information about this protein and its source genome.

Accession: VK055_3643
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK82198.1 rpoH
Status: annotated
Amino acids: 257
Structure source: AlphaFold + ColabFold

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: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: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:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 97.665
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 89.12

Selected Druggability evidence

AlphaFold / UniProt model

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 0.286

Structure A0A0H3H469

Pocket Pocket 1

P2Rank

Structure A0A0H3H469

Pocket No pockets

ColabFold model

FPocket 0.869 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 242 / 4744 genomes with a hit

Normalized 0.051

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

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: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: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: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.

35 records

Show feature table

Start	End	DB	Term	Name
185	255	FunFam	G3DSA:1.10.10.10:FF:000285	RNA polymerase sigma factor RpoH
173	256	SUPERFAMILY	SSF88659	Sigma3 and sigma4 domains of RNA polymerase sigma factors
173	256	InterPro	IPR013324	RNA polymerase sigma factor, region 3/4-like
100	257	FunFam	G3DSA:1.20.140.160:FF:000002	RNA polymerase sigma factor RpoH
1	257	PIRSF	PIRSF000770	SigK_SigE
1	257	InterPro	IPR000943	RNA polymerase sigma-70
21	254	NCBIfam	TIGR02937	sigma-70 family RNA polymerase sigma factor
21	254	InterPro	IPR014284	RNA polymerase sigma-70 like domain
1	257	Hamap	MF_00961	RNA polymerase sigma factor RpoH [rpoH].
1	257	InterPro	IPR012759	RNA polymerase sigma factor RpoH, proteobacteria
1	95	FunFam	G3DSA:1.20.120.1810:FF:000001	RNA polymerase sigma factor RpoH
201	253	Pfam	PF04545	Sigma-70, region 4
201	253	InterPro	IPR007630	RNA polymerase sigma-70 region 4
50	63	ProSitePatterns	PS00715	Sigma-70 factors family signature 1.
50	63	InterPro	IPR000943	RNA polymerase sigma-70
50	63	PRINTS	PR00046	Major sigma-70 factor signature
205	217	PRINTS	PR00046	Major sigma-70 factor signature
205	217	InterPro	IPR000943	RNA polymerase sigma-70
240	251	PRINTS	PR00046	Major sigma-70 factor signature
240	251	InterPro	IPR000943	RNA polymerase sigma-70
225	240	PRINTS	PR00046	Major sigma-70 factor signature
225	240	InterPro	IPR000943	RNA polymerase sigma-70
1	256	NCBIfam	TIGR02392	RNA polymerase sigma factor RpoH
1	256	InterPro	IPR012759	RNA polymerase sigma factor RpoH, proteobacteria
226	257	Coils	Coil	Coil
196	252	CDD	cd06171	Sigma70_r4
26	95	Pfam	PF04542	Sigma-70 region 2
26	95	InterPro	IPR007627	RNA polymerase sigma-70 region 2
1	95	SUPERFAMILY	SSF88946	Sigma2 domain of RNA polymerase sigma factors
1	95	InterPro	IPR013325	RNA polymerase sigma factor, region 2
225	251	ProSitePatterns	PS00716	Sigma-70 factors family signature 2.
225	251	InterPro	IPR000943	RNA polymerase sigma-70
1	95	Gene3D	G3DSA:1.20.120.1810	-
1	256	PANTHER	PTHR30376	SIGMA FACTOR RPOH HEAT SHOCK RELATED
100	257	Gene3D	G3DSA:1.20.140.160	-

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

0 + 2

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3H469	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_3643	ColabFold	—	—	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
1				0.286
6				0.024
2				0.005
15				0.004

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				0.869
12				0.018
3				0.004
9				0.0

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.