Target Pathogen

Overview

Basic information about this protein and its source genome.

Accession: PA3308
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: hepA PA3308 rapA
Status: annotated
Amino acids: 950
Structure source: AlphaFold

EC

3.6.4.-

GO

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0003682 Binding to chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0004386 Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix. GO:0016817 Catalysis of the hydrolysis of any acid anhydride. GO:0140750 A histone octamer slider activity that spaces nucleosomes along chromosomal DNA. This activity is involved in assembling chromatin in uniform nucleosome arrays to regulate transcription by RNA polymerases I, II, and III, as well as DNA replication, recombination and repair.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 30.256
Human E-value: 1.45e-06
Gut microbiome off-target: hit
Essential (DEG): N
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 0.814

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Enzyme Commission (EC)

1

3.6.4.-

Gene Ontology (GO)

10

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0003682 Binding to chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0004386 Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
GO:0016817 Catalysis of the hydrolysis of any acid anhydride.
GO:0140750 A histone octamer slider activity that spaces nucleosomes along chromosomal DNA. This activity is involved in assembling chromatin in uniform nucleosome arrays to regulate transcription by RNA polymerases I, II, and III, as well as DNA replication, recombination and repair.
GO:0031507 An epigenetic gene silencing mechanism in which chromatin is compacted into heterochromatin, resulting in a chromatin conformation refractory to transcription. This process starts with heterochromatin nucleation, its spreading, and ends with heterochromatin boundary formation.
GO:0045944 Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
GO:0140658 An activity, driven by ATP hydrolysis, that modulates the contacts between histones and DNA, resulting in a change in chromosome architecture within the nucleosomal array, leading to chromatin remodeling.

Sequence Features

Domain/signature hits from InterPro and related databases.

37 records

Show feature table

Start	End	DB	Term	Name
590	948	Pfam	PF12137	RNA polymerase recycling family C-terminal
590	948	InterPro	IPR022737	RNA polymerase recycling, bacterial, C-terminal
880	900	Coils	Coil	Coil
473	594	CDD	cd18793	SF2_C_SNF
4	950	Hamap	MF_01821	RNA polymerase-associated protein RapA [rapA].
4	950	InterPro	IPR023949	RNA polymerase-associated protein RapA
698	774	Gene3D	G3DSA:3.30.360.80	-
151	348	SMART	SM00487	ultradead3
151	348	InterPro	IPR014001	Helicase superfamily 1/2, ATP-binding domain
272	632	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
272	632	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
477	586	Pfam	PF00271	Helicase conserved C-terminal domain
477	586	InterPro	IPR001650	Helicase, C-terminal
475	629	ProSiteProfiles	PS51194	Superfamilies 1 and 2 helicase C-terminal domain profile.
475	629	InterPro	IPR001650	Helicase, C-terminal
858	937	Gene3D	G3DSA:6.10.140.1500	-
465	619	Gene3D	G3DSA:3.40.50.300	-
465	619	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
4	56	Gene3D	G3DSA:2.30.30.140	-
154	348	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
154	348	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
58	115	Gene3D	G3DSA:2.30.30.930	-
502	586	SMART	SM00490	helicmild6
502	586	InterPro	IPR001650	Helicase, C-terminal
169	389	Pfam	PF00176	SNF2-related domain
169	389	InterPro	IPR000330	SNF2, N-terminal
6	56	Pfam	PF18339	RapA N-terminal Tudor like domain 1
6	56	InterPro	IPR040765	RapA, N-terminal Tudor like domain 1
165	333	ProSiteProfiles	PS51192	Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile.
165	333	InterPro	IPR014001	Helicase superfamily 1/2, ATP-binding domain
58	119	Pfam	PF18337	RapA N-terminal Tudor like domain
58	119	InterPro	IPR040766	RapA, N-terminal Tudor-like domain 2
155	344	CDD	cd18011	DEXDc_RapA
620	669	Gene3D	G3DSA:6.10.140.2230	-
171	337	PANTHER	PTHR45766	DNA ANNEALING HELICASE AND ENDONUCLEASE ZRANB3 FAMILY MEMBER
151	430	Gene3D	G3DSA:3.40.50.10810	-
151	430	InterPro	IPR038718	SNF2-like, N-terminal domain superfamily

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 + 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 PA3308	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
3				0.287
1				0.283

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.

1 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
BEF	6JYL	P38144	66.0 Da LogP 0.88 TPSA 0.0	✓ Ro5	✓ Clean	`[Be-](F)(F)F`

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).

No virtual-screening candidates for this protein.

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.

PA3308