Protein profile

KP13_00773

DNA-directed RNA polymerase subunit alpha

Genome: KpKP13

Gene: AHE42386.1 rpoA Structure source: AlphaFold + ColabFold UniProt A0A0H3GYA3

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Amino acids 329

Annotations 7

Features 25

PDB binders 2

Druggability 0.82

Overview

Basic information about this protein and its source genome.

Accession: KP13_00773
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE42386.1 rpoA
Status: annotated
Amino acids: 329
Structure source: AlphaFold + ColabFold

2.7.7.6

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:0006351 The synthesis of an RNA transcript from a DNA template. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0046983 The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits. 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.

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 (%): 99.392
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 87.26

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 0.82

Structure A0A0H3GYA3

Pocket Pocket 10

P2Rank 0.054

Structure A0A0H3GYA3

Pocket Pocket 1

ColabFold model

FPocket 0.558 · Pocket 6

P2Rank 0.041 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 288 / 4744 genomes with a hit

Normalized 0.061

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: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:0006351 The synthesis of an RNA transcript from a DNA template.
GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0046983 The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
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.

Sequence Features

Domain/signature hits from InterPro and related databases.

25 records

Show feature table

Start	End	DB	Term	Name
24	316	NCBIfam	TIGR02027	DNA-directed RNA polymerase subunit alpha
24	316	InterPro	IPR011773	DNA-directed RNA polymerase, alpha subunit
6	231	SUPERFAMILY	SSF55257	RBP11-like subunits of RNA polymerase
6	231	InterPro	IPR036603	RNA polymerase, RBP11-like subunit
14	231	CDD	cd06928	RNAP_alpha_NTD
5	317	Hamap	MF_00059	DNA-directed RNA polymerase subunit alpha [rpoA].
5	317	InterPro	IPR011773	DNA-directed RNA polymerase, alpha subunit
15	220	Gene3D	G3DSA:3.30.1360.10	-
15	220	InterPro	IPR036603	RNA polymerase, RBP11-like subunit
53	177	Gene3D	G3DSA:2.170.120.12	-
53	177	InterPro	IPR036643	DNA-directed RNA polymerase, insert domain superfamily
245	308	Pfam	PF03118	Bacterial RNA polymerase, alpha chain C terminal domain
245	308	InterPro	IPR011260	RNA polymerase, alpha subunit, C-terminal
29	228	Pfam	PF01193	RNA polymerase Rpb3/Rpb11 dimerisation domain
29	228	InterPro	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type
53	178	SUPERFAMILY	SSF56553	Insert subdomain of RNA polymerase alpha subunit
53	178	InterPro	IPR036643	DNA-directed RNA polymerase, insert domain superfamily
53	177	FunFam	G3DSA:2.170.120.12:FF:000001	DNA-directed RNA polymerase subunit alpha
244	329	Gene3D	G3DSA:1.10.150.20	-
23	234	SMART	SM00662	rpoldneu2
23	234	InterPro	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type
251	325	SUPERFAMILY	SSF47789	C-terminal domain of RNA polymerase alpha subunit
244	329	FunFam	G3DSA:1.10.150.20:FF:000001	DNA-directed RNA polymerase subunit alpha
60	156	Pfam	PF01000	RNA polymerase Rpb3/RpoA insert domain
60	156	InterPro	IPR011262	DNA-directed RNA polymerase, insert 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

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_A0A0H3GYA3	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00773	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
10				0.82

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				1.44	0.019

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
6				0.558

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				1.27	0.013

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.