Protein profile

PA5556

ATP synthase subunit alpha

Genome: NC_002516.2

Gene: atpA PA5556 Structure source: AlphaFold UniProt Q9HT18

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Amino acids 514

Annotations 11

Features 35

PDB binders 10

Druggability 0.501

Overview

Basic information about this protein and its source genome.

Accession: PA5556
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: atpA PA5556
Status: annotated
Amino acids: 514
Structure source: AlphaFold

7.1.2.2

GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0045259 A proton-transporting two-sector ATPase complex that catalyzes the phosphorylation of ADP to ATP during oxidative phosphorylation. The complex comprises a membrane sector (F0) that carries out proton transport and a cytoplasmic compartment sector (F1) that catalyzes ATP synthesis by a rotational mechanism; the extramembrane sector (containing 3 a and 3 b subunits) is connected via the d-subunit to the membrane sector by several smaller subunits. Within this complex, the g and e subunits and the 9-12 c subunits rotate by consecutive 120 degree angles and perform parts of ATP synthesis. This movement is driven by the hydrogen ion electrochemical potential gradient. GO:0043531 Binding to ADP, adenosine 5'-diphosphate. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0046933 Enables the synthesis of ATP from ADP and phosphate by the transfer of protons from one side of a membrane to the other by a rotational mechanism driven by a gradient according to the reaction: ADP + phosphate + 5 H+(out) => ATP + H2O + 4 H+(in). GO:0015986 The chemical reactions and pathways resulting in the formation of ATP driven by transport of protons across a membrane to generate an electrochemical gradient (proton-motive force).

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 59.211
Human E-value: 1.17e-52
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 0.501

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)

7.1.2.2

Gene Ontology (GO)

GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0045259 A proton-transporting two-sector ATPase complex that catalyzes the phosphorylation of ADP to ATP during oxidative phosphorylation. The complex comprises a membrane sector (F0) that carries out proton transport and a cytoplasmic compartment sector (F1) that catalyzes ATP synthesis by a rotational mechanism; the extramembrane sector (containing 3 a and 3 b subunits) is connected via the d-subunit to the membrane sector by several smaller subunits. Within this complex, the g and e subunits and the 9-12 c subunits rotate by consecutive 120 degree angles and perform parts of ATP synthesis. This movement is driven by the hydrogen ion electrochemical potential gradient.
GO:0043531 Binding to ADP, adenosine 5'-diphosphate.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0046933 Enables the synthesis of ATP from ADP and phosphate by the transfer of protons from one side of a membrane to the other by a rotational mechanism driven by a gradient according to the reaction: ADP + phosphate + 5 H+(out) => ATP + H2O + 4 H+(in).
GO:0015986 The chemical reactions and pathways resulting in the formation of ATP driven by transport of protons across a membrane to generate an electrochemical gradient (proton-motive force).
GO:1902600 The directed movement of a proton across a membrane.
GO:0032559 Binding to an adenyl ribonucleotide, any compound consisting of adenosine esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose moiety.
GO:0045261 OBSOLETE. The sector of a hydrogen-transporting ATP synthase complex in which the catalytic activity resides; it comprises the catalytic core and central stalk, and is peripherally associated with a membrane, such as the plasma membrane or the mitochondrial inner membrane, when the entire ATP synthase is assembled.
GO:0046034 The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator.

Sequence Features

Domain/signature hits from InterPro and related databases.

35 records

Show feature table

Start	End	DB	Term	Name
1	94	Gene3D	G3DSA:2.40.30.20	-
1	94	InterPro	IPR023366	ATP synthase subunit alpha, N-terminal domain-like superfamily
384	514	FunFam	G3DSA:1.20.150.20:FF:000001	ATP synthase subunit alpha
384	512	SUPERFAMILY	SSF47917	C-terminal domain of alpha and beta subunits of F1 ATP synthase
150	376	Pfam	PF00006	ATP synthase alpha/beta family, nucleotide-binding domain
150	376	InterPro	IPR000194	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain
95	379	CDD	cd01132	F1-ATPase_alpha_CD
95	379	InterPro	IPR033732	ATP synthase, F1 complex, alpha subunit nucleotide-binding domain
384	514	Gene3D	G3DSA:1.20.150.20	-
384	514	InterPro	IPR038376	ATP synthase, alpha subunit, C-terminal domain superfamily
3	510	PANTHER	PTHR48082	ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
3	510	InterPro	IPR005294	ATP synthase, F1 complex, alpha subunit
1	94	FunFam	G3DSA:2.40.30.20:FF:000001	ATP synthase subunit alpha
97	382	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
97	382	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
2	514	PIRSF	PIRSF039088	F_ATPase_subunit_alpha
2	514	InterPro	IPR005294	ATP synthase, F1 complex, alpha subunit
95	383	Gene3D	G3DSA:3.40.50.300	-
95	383	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
11	95	SUPERFAMILY	SSF50615	N-terminal domain of alpha and beta subunits of F1 ATP synthase
11	95	InterPro	IPR036121	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily
387	511	CDD	cd18113	ATP-synt_F1_alpha_C
387	511	InterPro	IPR000793	ATP synthase, alpha subunit, C-terminal
2	513	Hamap	MF_01346	ATP synthase subunit alpha [atpA].
2	513	InterPro	IPR005294	ATP synthase, F1 complex, alpha subunit
4	513	NCBIfam	TIGR00962	F0F1 ATP synthase subunit alpha
4	513	InterPro	IPR005294	ATP synthase, F1 complex, alpha subunit
383	508	Pfam	PF00306	ATP synthase alpha/beta chain, C terminal domain
383	508	InterPro	IPR000793	ATP synthase, alpha subunit, C-terminal
30	93	Pfam	PF02874	ATP synthase alpha/beta family, beta-barrel domain
30	93	InterPro	IPR004100	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain
28	94	CDD	cd18116	ATP-synt_F1_alpha_N
95	383	FunFam	G3DSA:3.40.50.300:FF:000002	ATP synthase subunit alpha
367	376	ProSitePatterns	PS00152	ATP synthase alpha and beta subunits signature.
367	376	InterPro	IPR020003	ATPase, alpha/beta subunit, nucleotide-binding domain, active site

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

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Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA5556	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
2				0.501
9				0.448
4				0.415
3				0.227

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.

61 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
AF3	1E1R	P19483	84.0 Da LogP 0.88 TPSA 0.0	✓ Ro5	✓ Clean	`F[Al](F)F`
ALF	1H8E	P19483	103.0 Da LogP 1.30 TPSA 0.0	✓ Ro5	✓ Clean	`F[Al-](F)(F)F`
ANP	2HLD	P07251	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)…`
AUR	1COW	P19483	460.5 Da LogP 3.10 TPSA 104.4	✓ Ro5	✓ Clean	`CC[C@@H]1[C@]2([C@H]([C@@](O1)([C@H]([C@@H](O2)…`
AZI	2CK3	P19483	42.0 Da LogP 0.87 TPSA 58.7	✓ Ro5	Alert	`[N-]=[N+]=[N-]`
BEF	1W0J	P19483	66.0 Da LogP 0.88 TPSA 0.0	✓ Ro5	✓ Clean	`[Be-](F)(F)F`
QUE	2JJ2	P19483	302.2 Da LogP 1.99 TPSA 131.4	✓ Ro5	Alert	`c1cc(c(cc1C2=C(C(=O)c3c(cc(cc3O2)O)O)O)O)O`
STL	2JIZ	P19483	228.2 Da LogP 2.97 TPSA 60.7	✓ Ro5	✓ Clean	`c1cc(ccc1\C=C\c2cc(cc(c2)O)O)O`
TS6	4YXW	P19483	114.1 Da LogP 0.01 TPSA 57.5	✓ Ro5	✓ Clean	`OP(=O)(O)S`
VO4	2F43	P15999	114.9 Da LogP -3.69 TPSA 86.2	✓ Ro5	✓ Clean	`[O-][V](=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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL2063416	P25705	—	716.8 Da LogP 1.65 TPSA 238.1	3 viol.	Alert	`O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@@H]21)NCCOCCO…`

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
ZINC12353732	1.000	228.2 Da LogP 2.97 TPSA 60.7	✓ Ro5	✓ Clean	`Oc1ccc(/C=C\c2cc(O)cc(O)c2)cc1`
ZINC1857524289	1.000	228.2 Da LogP 2.97 TPSA 60.7	✓ Ro5	✓ Clean	`Oc1ccc(C=Cc2cc(O)cc(O)c2)cc1`
ZINC6787	1.000	228.2 Da LogP 2.97 TPSA 60.7	✓ Ro5	✓ Clean	`Oc1ccc(/C=C/c2cc(O)cc(O)c2)cc1`
ZINC12360002	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…`
ZINC12360703	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…`
ZINC12503599	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…`
ZINC16546165	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)(…`
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)…`
ZINC4806433	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…`
ZINC53683898	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(=…`
ZINC8586019	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)…`
ZINC8586020	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(=…`
ZINC8586021	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…`
ZINC8586022	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(=…`
ZINC3874317	0.757	318.2 Da LogP 1.69 TPSA 151.6	1 viol.	Alert	`O=c1c(O)c(-c2cc(O)c(O)c(O)c2)oc2cc(O)cc(O)c12`
ZINC13518964	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1571045	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC2046931	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC4806442	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8613167	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC13319959	0.737	212.2 Da LogP 3.27 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(/C=C\c2ccc(O)cc2)cc1`
ZINC1510311	0.737	212.2 Da LogP 3.27 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(/C=C/c2ccc(O)cc2)cc1`
ZINC1875408805	0.737	212.2 Da LogP 3.27 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(C=Cc2ccc(O)cc2)cc1`
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@@…`
ZINC12503850	0.726	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141161066	0.726	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141163786	0.726	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC4228246	0.726	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OS(=O…`
ZINC34544488	0.720	230.2 Da LogP 3.41 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(/C=C/c2cc(O)cc(F)c2)cc1`
ZINC120273	0.718	270.2 Da LogP 2.58 TPSA 90.9	✓ Ro5	✓ Clean	`O=c1c(O)c(-c2ccccc2)oc2cc(O)cc(O)c12`
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](…`
ZINC2561223	0.708	291.1 Da LogP 4.03 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1cc(O)cc(/C=C/c2ccc(Br)cc2)c1`
ZINC49588452	0.708	246.7 Da LogP 3.92 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1cc(O)cc(/C=C/c2ccc(Cl)cc2)c1`
ZINC71622042	0.708	246.7 Da LogP 3.92 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1cc(O)cc(/C=C\c2ccc(Cl)cc2)c1`
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)…`
ZINC901115	0.696	212.2 Da LogP 3.27 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1cc(O)cc(/C=C/c2ccccc2)c1`
ZINC9147134	0.696	212.2 Da LogP 3.27 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1cc(O)cc(/C=C\c2ccccc2)c1`
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)…`
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)…`

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.