Target Pathogen

Overview

Basic information about this protein and its source genome.

Accession: PA4609
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA4609 radA
Status: annotated
Amino acids: 453
Structure source: AlphaFold

EC

3.6.4.-

GO

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0140664 A molecule that recognises toxic DNA structures, and initiates a signaling response, driven by ATP hydrolysis. GO:0003684 Binding to damaged DNA. GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0008270 Binding to a zinc ion (Zn). GO:0000725 A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous DNA region.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Unknown

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 0.758

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MAKAKRMYGCTECGATFPKWAGQCADCGAWNTLVETVVEAAPSGSGRGGWAGQQANLKTLAEVSVEEMPRFTTGSTELDRVLGGGLVDGSVVLIGGDPGIGKSTILLQTLCNLASRVPALYVTGEESQQQVAMRARRLSLPEDKLKVMTETSIETIIATARQEQPRVMVIDSIQTIFTEQLQSAPGGVAQVRESAAMLVRYAKQSGTAIFLVGHVTKEGALAGPRVLEHMVDTVLYFEGESDGRLRLLRAVKNRFGAVNELGVFGMTDKGLKEVSNPSAIFLTRAQEAVPGSVVMATWEGSRPMLVEVQALVDTSHLANPRRVTLGLDQNRLAMLLAVLHRHGGIPTYDQDVFLNVVGGVKVLETASDLALMAAVMSSLRNRPLPHDLLVFGEVGLSGEVRPVPSGQERLKEAGKHGFKRAIVPLGNAPKEAPAGLQVIAVTRLEQALDALFE

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

3.6.4.-

Gene Ontology (GO)

9

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0140664 A molecule that recognises toxic DNA structures, and initiates a signaling response, driven by ATP hydrolysis.
GO:0003684 Binding to damaged DNA.
GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
GO:0008270 Binding to a zinc ion (Zn).
GO:0000725 A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous DNA region.
GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.

Sequence Features

Domain/signature hits from InterPro and related databases.

31 records

Show feature table

Start	End	DB	Term	Name
21	452	Hamap	MF_01498	DNA repair protein RadA [radA].
21	452	InterPro	IPR004504	DNA repair protein RadA
296	453	FunFam	G3DSA:3.30.230.10:FF:000011	DNA repair protein RadA
281	453	Gene3D	G3DSA:3.30.230.10	-
281	453	InterPro	IPR014721	Ribosomal protein S5 domain 2-type fold, subgroup
57	271	Gene3D	G3DSA:3.40.50.300	-
57	271	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
8	274	CDD	cd01121	RadA_SMS_N
67	215	ProSiteProfiles	PS50162	RecA family profile 1.
67	215	InterPro	IPR020588	DNA recombination and repair protein RecA-like, ATP-binding domain
1	448	NCBIfam	TIGR00416	DNA repair protein RadA
1	448	InterPro	IPR004504	DNA repair protein RadA
3	452	PANTHER	PTHR32472	DNA REPAIR PROTEIN RADA
8	35	Pfam	PF18073	Rubredoxin metal binding domain
8	35	InterPro	IPR041166	LapB, rubredoxin metal binding domain
252	452	SUPERFAMILY	SSF54211	Ribosomal protein S5 domain 2-like
252	452	InterPro	IPR020568	Ribosomal protein S5 domain 2-type fold
361	427	Pfam	PF13541	Subunit ChlI of Mg-chelatase
60	272	FunFam	G3DSA:3.40.50.300:FF:000050	DNA repair protein RadA
66	286	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
66	286	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
74	219	Pfam	PF13481	AAA domain
88	241	SMART	SM00382	AAA_5
88	241	InterPro	IPR003593	AAA+ ATPase domain
10	34	PRINTS	PR01874	DNA repair protein radA signature
121	138	PRINTS	PR01874	DNA repair protein radA signature
171	195	PRINTS	PR01874	DNA repair protein radA signature
80	108	PRINTS	PR01874	DNA repair protein radA signature
210	238	PRINTS	PR01874	DNA repair protein radA signature
319	342	PRINTS	PR01874	DNA repair protein radA signature
245	271	PRINTS	PR01874	DNA repair protein radA signature

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 PA4609	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
4				0.758
8				0.464
2				0.245

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
POP	2W0M	Q97VZ8	176.0 Da LogP -2.08 TPSA 129.9	✓ Ro5	✓ Clean	`O[P@@](=O)([O-])O[P@@](=O)(O)[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).

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.

PA4609