Protein profile

PA4238

DNA-directed RNA polymerase subunit alpha

Genome: NC_002516.2

Gene: rpoA PA4238 Structure source: AlphaFold UniProt O52760

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Amino acids 333

Annotations 7

Features 25

PDB binders 2

Druggability 0.821

Overview

Basic information about this protein and its source genome.

Accession: PA4238
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: rpoA PA4238
Status: annotated
Amino acids: 333
Structure source: AlphaFold

2.7.7.6

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0000428 A protein complex that possesses DNA-directed RNA polymerase activity. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0003899 Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'. GO:0046983 The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits. GO:0006351 The synthesis of an RNA transcript from a DNA template.

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 0.821

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

2.7.7.6

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0000428 A protein complex that possesses DNA-directed RNA polymerase activity.
GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0003899 Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
GO:0046983 The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
GO:0006351 The synthesis of an RNA transcript from a DNA template.

Sequence Features

Domain/signature hits from InterPro and related databases.

25 records

Show feature table

Start	End	DB	Term	Name
53	176	Gene3D	G3DSA:2.170.120.12	-
53	176	InterPro	IPR036643	DNA-directed RNA polymerase, insert domain superfamily
243	328	Gene3D	G3DSA:1.10.150.20	-
53	176	FunFam	G3DSA:2.170.120.12:FF:000001	DNA-directed RNA polymerase subunit alpha
29	227	Pfam	PF01193	RNA polymerase Rpb3/Rpb11 dimerisation domain
29	227	InterPro	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type
250	323	SUPERFAMILY	SSF47789	C-terminal domain of RNA polymerase alpha subunit
64	155	Pfam	PF01000	RNA polymerase Rpb3/RpoA insert domain
64	155	InterPro	IPR011262	DNA-directed RNA polymerase, insert domain
23	233	SMART	SM00662	rpoldneu2
23	233	InterPro	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type
243	307	Pfam	PF03118	Bacterial RNA polymerase, alpha chain C terminal domain
243	307	InterPro	IPR011260	RNA polymerase, alpha subunit, C-terminal
15	219	Gene3D	G3DSA:3.30.1360.10	-
15	219	InterPro	IPR036603	RNA polymerase, RBP11-like subunit
53	177	SUPERFAMILY	SSF56553	Insert subdomain of RNA polymerase alpha subunit
53	177	InterPro	IPR036643	DNA-directed RNA polymerase, insert domain superfamily
242	328	FunFam	G3DSA:1.10.150.20:FF:000001	DNA-directed RNA polymerase subunit alpha
14	230	CDD	cd06928	RNAP_alpha_NTD
5	316	Hamap	MF_00059	DNA-directed RNA polymerase subunit alpha [rpoA].
5	316	InterPro	IPR011773	DNA-directed RNA polymerase, alpha subunit
6	232	SUPERFAMILY	SSF55257	RBP11-like subunits of RNA polymerase
6	232	InterPro	IPR036603	RNA polymerase, RBP11-like subunit
24	315	NCBIfam	TIGR02027	DNA-directed RNA polymerase subunit alpha
24	315	InterPro	IPR011773	DNA-directed RNA polymerase, alpha subunit

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 PA4238	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				0.821
6				0.705
1				0.465

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.

52 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	6XLJ	P0A7Z4	430.2 Da LogP 3.06 TPSA 0.0	✓ Ro5	✓ Clean	`c1ccc(cc1)[Sb+](c2ccccc2)(c3ccccc3)c4ccccc4`
1N7	6N58	P0A7Z4	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…`

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
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@…`
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]…`
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@…`
ZINC118912651	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…`
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@…`
ZINC17654510	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@…`
ZINC1857777516	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@…`
ZINC2060999621	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…`
ZINC53683926	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@…`
ZINC61389426	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@…`
ZINC61389432	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…`
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@…`
ZINC1888994477	0.633	447.7 Da LogP 3.67 TPSA 89.8	✓ Ro5	✓ Clean	`C=CCNC(=O)CC[C@@H](C)[C@H]1CC[C@@H]2[C@H]3[C@H]…`
ZINC1888994478	0.633	447.7 Da LogP 3.67 TPSA 89.8	✓ Ro5	✓ Clean	`C=CCNC(=O)CC[C@@H](C)[C@H]1CC[C@@H]2[C@H]3[C@H]…`
ZINC1888994479	0.633	447.7 Da LogP 3.67 TPSA 89.8	✓ Ro5	✓ Clean	`C=CCNC(=O)CC[C@@H](C)[C@H]1CC[C@@H]2[C@@H]3[C@H…`
ZINC1888994480	0.633	447.7 Da LogP 3.67 TPSA 89.8	✓ Ro5	✓ Clean	`C=CCNC(=O)CC[C@@H](C)[C@H]1CC[C@@H]2[C@@H]3[C@H…`
ZINC118912563	0.618	444.6 Da LogP 2.86 TPSA 115.1	✓ Ro5	✓ Clean	`C[C@@H](CCS(=O)(=O)O)[C@H]1CC[C@H]2[C@H]3[C@H](…`
ZINC118912564	0.618	444.6 Da LogP 2.86 TPSA 115.1	✓ Ro5	✓ Clean	`C[C@H](CCS(=O)(=O)O)[C@H]1CC[C@H]2[C@H]3[C@H](C…`
ZINC1857533481	0.618	444.6 Da LogP 2.86 TPSA 115.1	✓ Ro5	✓ Clean	`C[C@@H](CCS(=O)(=O)O)[C@@H]1CC[C@H]2[C@H]3[C@H]…`
ZINC1857533482	0.618	444.6 Da LogP 2.86 TPSA 115.1	✓ Ro5	✓ Clean	`C[C@H](CCS(=O)(=O)O)[C@@H]1CC[C@H]2[C@H]3[C@H](…`
ZINC253534390	0.618	444.6 Da LogP 2.86 TPSA 115.1	✓ Ro5	✓ Clean	`C[C@H](CCS(=O)(=O)O)[C@@H]1CC[C@@H]2[C@H]3[C@H]…`
ZINC253534391	0.618	444.6 Da LogP 2.86 TPSA 115.1	✓ Ro5	✓ Clean	`C[C@@H](CCS(=O)(=O)O)[C@@H]1CC[C@@H]2[C@H]3[C@H…`
ZINC253534392	0.618	444.6 Da LogP 2.86 TPSA 115.1	✓ Ro5	✓ Clean	`C[C@@H](CCS(=O)(=O)O)[C@@H]1CC[C@@H]2[C@H]3[C@H…`
ZINC253534393	0.618	444.6 Da LogP 2.86 TPSA 115.1	✓ Ro5	✓ Clean	`C[C@H](CCS(=O)(=O)O)[C@@H]1CC[C@@H]2[C@H]3[C@H]…`
ZINC253497472	0.605	408.6 Da LogP 3.45 TPSA 98.0	✓ Ro5	✓ Clean	`C[C@@H](CCC(=O)O)[C@@H]1CC[C@@H]2[C@H]3[C@H](O)…`
ZINC253497474	0.605	408.6 Da LogP 3.45 TPSA 98.0	✓ Ro5	✓ Clean	`C[C@@H](CCC(=O)O)[C@@H]1CC[C@@H]2[C@H]3[C@H](O)…`
ZINC29747682	0.605	408.6 Da LogP 3.45 TPSA 98.0	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)O)[C@H]1CC[C@H]2[C@H]3[C@H](C[C@H…`
ZINC40164313	0.605	408.6 Da LogP 3.45 TPSA 98.0	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)O)[C@H]1CC[C@H]2[C@@H]3[C@@H](O)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.