Protein profile

PA3466

ATP-dependent RNA helicase

Genome: NC_002516.2

Gene: PA3466 Structure source: AlphaFold UniProt Q9HYE0

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Amino acids 446

Annotations 5

Features 26

PDB binders 5

Druggability 0.653

Overview

Basic information about this protein and its source genome.

Accession: PA3466
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA3466
Status: annotated
Amino acids: 446
Structure source: AlphaFold

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0003676 Binding to a nucleic acid. GO:0003724 Unwinding of an RNA helix, driven by ATP hydrolysis.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 56.41
Human E-value: 4.84e-07
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 0.653

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
GO:0003676 Binding to a nucleic acid.
GO:0003724 Unwinding of an RNA helix, driven by ATP hydrolysis.

Sequence Features

Domain/signature hits from InterPro and related databases.

26 records

Show feature table

Start	End	DB	Term	Name
387	446	MobiDBLite	mobidb-lite	consensus disorder prediction
29	192	Pfam	PF00270	DEAD/DEAH box helicase
29	192	InterPro	IPR011545	DEAD/DEAH box helicase domain
237	382	ProSiteProfiles	PS51194	Superfamilies 1 and 2 helicase C-terminal domain profile.
237	382	InterPro	IPR001650	Helicase, C-terminal
16	211	CDD	cd00268	DEADc
222	352	CDD	cd18787	SF2_C_DEAD
36	209	ProSiteProfiles	PS51192	Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile.
36	209	InterPro	IPR014001	Helicase superfamily 1/2, ATP-binding domain
216	421	Gene3D	G3DSA:3.40.50.300	-
216	421	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
155	163	ProSitePatterns	PS00039	DEAD-box subfamily ATP-dependent helicases signature.
155	163	InterPro	IPR000629	ATP-dependent RNA helicase DEAD-box, conserved site
7	393	PANTHER	PTHR47959	ATP-DEPENDENT RNA HELICASE RHLE-RELATED
262	343	SMART	SM00490	helicmild6
262	343	InterPro	IPR001650	Helicase, C-terminal
24	225	SMART	SM00487	ultradead3
24	225	InterPro	IPR014001	Helicase superfamily 1/2, ATP-binding domain
78	360	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
78	360	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
238	343	Pfam	PF00271	Helicase conserved C-terminal domain
238	343	InterPro	IPR001650	Helicase, C-terminal
5	33	ProSiteProfiles	PS51195	DEAD-box RNA helicase Q motif profile.
5	33	InterPro	IPR014014	RNA helicase, DEAD-box type, Q motif
2	213	Gene3D	G3DSA:3.40.50.300	-
2	213	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase

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 PA3466	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
1				0.653

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.

56 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
ANP	5E7M	O00571	506.2 Da LogP -2.06 TPSA 281.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
BEF	6UV1	Q92841	66.0 Da LogP 0.88 TPSA 0.0	✓ Ro5	✓ Clean	`[Be-](F)(F)F`
CXS	4NHO	Q9BUQ8	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`C1CCC(CC1)NCCCS(=O)(=O)O`
IHP	6QX9	Q9BUQ8	660.0 Da LogP -3.13 TPSA 400.6	3 viol.	✓ Clean	`C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)O…`
M7M	6QX9	Q9BUQ8	487.3 Da LogP -2.28 TPSA 218.4	2 viol.	✓ Clean	`CN1CN(C2=C1C(=O)N=C(N2)N(C)C)[C@H]3[C@@H]([C@@H…`

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL501187	O00571	—	563.7 Da LogP 3.76 TPSA 162.6	1 viol.	✓ Clean	`CCCCCCCCCCCCCCCCCCNc1nc(=O)c2ncn([C@@H]3O[C@H](…`

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
ZINC2004372	1.000	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC1CCCCC1`
ZINC38364153	0.926	235.3 Da LogP 1.58 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC1CCCCC1`
ZINC31977053	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC1710230	0.786	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC1CCCCC1`
ZINC113264413	0.778	317.4 Da LogP 3.98 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(-c2ccc(-c3ccccc3)cc2)cc1)C(=O)O`
ZINC113264415	0.778	317.4 Da LogP 3.98 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(-c2ccc(-c3ccccc3)cc2)cc1)C(=O)O`
ZINC2244337	0.778	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(-c2ccccc2)cc1)C(=O)O`
ZINC2244338	0.778	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(-c2ccccc2)cc1)C(=O)O`
ZINC1834294	0.769	252.3 Da LogP -0.40 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1cccc(C[C@H](N)C(=O)O)c1)C(=O)O`
ZINC1834295	0.769	252.3 Da LogP -0.40 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1cccc(C[C@@H](N)C(=O)O)c1)C(=O)O`
ZINC1834297	0.769	252.3 Da LogP -0.40 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](Cc1cccc(C[C@@H](N)C(=O)O)c1)C(=O)O`
ZINC39351856	0.731	328.4 Da LogP 1.26 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(-c2ccc(C[C@H](N)C(=O)O)cc2)cc1)C…`
ZINC4096224	0.729	346.2 Da LogP -1.90 TPSA 191.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](N)(=O)O)[C@@…`
ZINC2561081	0.724	269.3 Da LogP 1.87 TPSA 80.4	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(C(=O)c2ccccc2)cc1)C(=O)O`
ZINC2561082	0.724	269.3 Da LogP 1.87 TPSA 80.4	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(C(=O)c2ccccc2)cc1)C(=O)O`
ZINC13556870	0.722	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@@H](O)[C@@H](O)[C@H](O)[C@@H…`
ZINC71789368	0.722	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@H](OP(=O)(O)O)[C@@H](O)[C@H]…`
ZINC71792243	0.722	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@H](O)[C@@H](O)[C@@H](O)[C@@H…`
ZINC105372833	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC105372837	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC17107643	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC204538551	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC100015956	0.706	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@H](O)[C@@H](OP(=O)(O)O)[C@H]…`
ZINC100015959	0.706	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@H](O)[C@@H](OP(=O)(O)O)[C@H]…`
ZINC100016166	0.706	340.1 Da LogP -3.60 TPSA 214.4	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1[C@@H](O)[C@@H](O)[C@@H](OP(=O…`
ZINC100590871	0.706	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@H](O)[C@H](OP(=O)(O)O)[C@H](…`
ZINC1501016356	0.706	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)OC1C(O)[C@H](OP(=O)(O)O)C(O)[C@H](OP(=…`
ZINC31475423	0.703	434.3 Da LogP -2.99 TPSA 238.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@@](=O)(O)OC(=O)…`
ZINC113539705	0.700	265.3 Da LogP 2.04 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(C#Cc2ccccc2)cc1)C(=O)O`
ZINC113539708	0.700	265.3 Da LogP 2.04 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(C#Cc2ccccc2)cc1)C(=O)O`
ZINC116910786	0.700	269.3 Da LogP 3.06 TPSA 88.0	✓ Ro5	Alert	`N[C@@H](Cc1ccc(/N=N/c2ccccc2)cc1)C(=O)O`
ZINC29566843	0.700	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1cccc(-c2ccccc2)c1)C(=O)O`
ZINC29570997	0.700	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1cccc(-c2ccccc2)c1)C(=O)O`
ZINC44283581	0.700	257.3 Da LogP 2.43 TPSA 72.5	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(Oc2ccccc2)cc1)C(=O)O`
ZINC44283583	0.700	257.3 Da LogP 2.43 TPSA 72.5	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(Oc2ccccc2)cc1)C(=O)O`
ZINC105469665	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)CP(=O…`
ZINC13527614	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)CP(=O)…`
ZINC219330894	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)CP(=O)…`
ZINC3873852	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)CP(=O)…`
ZINC3873853	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@](=O)(O)CP(=O…`
ZINC3873854	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)CP(=O)…`
ZINC3873855	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@](=O)(O)CP(=O…`
ZINC2111574	0.692	252.3 Da LogP -0.40 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1C[C@H](N)C(=O)O)C(=O)O`
ZINC2111575	0.692	252.3 Da LogP -0.40 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1C[C@@H](N)C(=O)O)C(=O)O`
ZINC2111578	0.692	252.3 Da LogP -0.40 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](Cc1ccccc1C[C@@H](N)C(=O)O)C(=O)O`
ZINC12648269	0.690	237.3 Da LogP 0.73 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](C[C@@H](Cc1ccccc1)C(=O)O)C(=O)O`
ZINC1616445	0.690	354.5 Da LogP 0.36 TPSA 110.2	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1)C(=O)NCCNC(=O)[C@H](N)Cc1cccc…`
ZINC1616446	0.690	354.5 Da LogP 0.36 TPSA 110.2	✓ Ro5	✓ Clean	`N[C@H](Cc1ccccc1)C(=O)NCCNC(=O)[C@H](N)Cc1ccccc1`
ZINC1616447	0.690	354.5 Da LogP 0.36 TPSA 110.2	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1)C(=O)NCCNC(=O)[C@@H](N)Cc1ccc…`
ZINC5225893	0.690	237.3 Da LogP 0.73 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](C[C@H](Cc1ccccc1)C(=O)O)C(=O)O`

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.