Protein profile

PA5554

ATP synthase subunit beta

Genome: NC_002516.2

Gene: atpD PA5554 Structure source: AlphaFold UniProt Q9HT20

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Amino acids 458

Annotations 10

Features 28

PDB binders 11

Druggability 0.75

Overview

Basic information about this protein and its source genome.

Accession: PA5554
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: atpD PA5554
Status: annotated
Amino acids: 458
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: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:1902600 The directed movement of a proton across a membrane. 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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 77.381
Human E-value: 5.35e-85
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 0.75

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 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: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:1902600 The directed movement of a proton across a membrane.
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: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: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.

28 records

Show feature table

Start	End	DB	Term	Name
6	71	Pfam	PF02874	ATP synthase alpha/beta family, beta-barrel domain
6	71	InterPro	IPR004100	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain
3	458	NCBIfam	TIGR01039	F0F1 ATP synthase subunit beta
3	458	InterPro	IPR005722	ATP synthase, F1 complex, beta subunit
344	458	Gene3D	G3DSA:1.10.1140.10	-
344	458	InterPro	IPR024034	ATPase, F1/V1 complex, beta/alpha subunit, C-terminal
343	458	FunFam	G3DSA:1.10.1140.10:FF:000001	ATP synthase subunit beta
1	73	Gene3D	G3DSA:2.40.10.170	-
343	457	SUPERFAMILY	SSF47917	C-terminal domain of alpha and beta subunits of F1 ATP synthase
2	74	CDD	cd18115	ATP-synt_F1_beta_N
128	340	Pfam	PF00006	ATP synthase alpha/beta family, nucleotide-binding domain
128	340	InterPro	IPR000194	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain
331	340	ProSitePatterns	PS00152	ATP synthase alpha and beta subunits signature.
331	340	InterPro	IPR020003	ATPase, alpha/beta subunit, nucleotide-binding domain, active site
3	458	PANTHER	PTHR15184	ATP SYNTHASE
2	72	SUPERFAMILY	SSF50615	N-terminal domain of alpha and beta subunits of F1 ATP synthase
2	72	InterPro	IPR036121	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily
75	345	CDD	cd01133	F1-ATPase_beta_CD
1	458	Hamap	MF_01347	ATP synthase subunit beta [atpB].
1	458	InterPro	IPR005722	ATP synthase, F1 complex, beta subunit
347	454	CDD	cd18110	ATP-synt_F1_beta_C
140	325	SMART	SM00382	AAA_5
140	325	InterPro	IPR003593	AAA+ ATPase domain
75	346	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
75	346	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
74	342	FunFam	G3DSA:3.40.50.300:FF:000004	ATP synthase subunit beta
74	343	Gene3D	G3DSA:3.40.50.300	-
74	343	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 PA5554	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				0.75
5				0.652

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.

62 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	P00829	84.0 Da LogP 0.88 TPSA 0.0	✓ Ro5	✓ Clean	`F[Al](F)F`
ALF	1H8E	P00829	103.0 Da LogP 1.30 TPSA 0.0	✓ Ro5	✓ Clean	`F[Al-](F)(F)F`
ANP	1BMF	P00829	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	P00829	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	P00829	42.0 Da LogP 0.87 TPSA 58.7	✓ Ro5	Alert	`[N-]=[N+]=[N-]`
BEF	1W0J	P00829	66.0 Da LogP 0.88 TPSA 0.0	✓ Ro5	✓ Clean	`[Be-](F)(F)F`
DCW	1E79	P00829	224.3 Da LogP 2.95 TPSA 41.1	✓ Ro5	✓ Clean	`C1CCC(CC1)NC(=O)NC2CCCCC2`
QUE	2JJ2	P00829	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	P00829	228.2 Da LogP 2.97 TPSA 60.7	✓ Ro5	✓ Clean	`c1cc(ccc1\C=C\c2cc(cc(c2)O)O)O`
TS6	4YXW	P00829	114.1 Da LogP 0.01 TPSA 57.5	✓ Ro5	✓ Clean	`OP(=O)(O)S`
VO4	2F43	P10719	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	P06576	—	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`
ZINC157375	1.000	224.3 Da LogP 2.95 TPSA 41.1	✓ Ro5	✓ Clean	`O=C(NC1CCCCC1)NC1CCCCC1`
ZINC1857524289	1.000	228.2 Da LogP 2.97 TPSA 60.7	✓ Ro5	✓ Clean	`Oc1ccc(C=Cc2cc(O)cc(O)c2)cc1`
ZINC370205	1.000	252.4 Da LogP 3.73 TPSA 41.1	✓ Ro5	✓ Clean	`O=C(NC1CCCCCCC1)NC1CCCCC1`
ZINC376044	1.000	238.4 Da LogP 3.34 TPSA 41.1	✓ Ro5	✓ Clean	`O=C(NC1CCCCCC1)NC1CCCCC1`
ZINC3869685	1.000	302.2 Da LogP 1.99 TPSA 131.4	✓ Ro5	Alert	`O=c1c(O)c(-c2ccc(O)c(O)c2)oc2cc(O)cc(O)c12`
ZINC44123745	1.000	252.4 Da LogP 3.73 TPSA 41.1	✓ Ro5	✓ Clean	`O=C(NC1CCCCCC1)NC1CCCCCC1`
ZINC6787	1.000	228.2 Da LogP 2.97 TPSA 60.7	✓ Ro5	✓ Clean	`Oc1ccc(/C=C/c2cc(O)cc(O)c2)cc1`
ZINC48844720	0.944	210.3 Da LogP 2.56 TPSA 41.1	✓ Ro5	✓ Clean	`O=C(NC1CCCCCCC1)NC1CC1`
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(=…`
ZINC12343510	0.810	364.5 Da LogP 3.56 TPSA 82.3	✓ Ro5	✓ Clean	`O=C(NC1CCCCC1)N[C@H]1CCCC[C@H]1NC(=O)NC1CCCCC1`
ZINC637766	0.810	364.5 Da LogP 3.56 TPSA 82.3	✓ Ro5	✓ Clean	`O=C(NC1CCCCC1)N[C@@H]1CCCC[C@H]1NC(=O)NC1CCCCC1`
ZINC637768	0.810	364.5 Da LogP 3.56 TPSA 82.3	✓ Ro5	✓ Clean	`O=C(NC1CCCCC1)N[C@H]1CCCC[C@@H]1NC(=O)NC1CCCCC1`
ZINC35115081	0.773	240.3 Da LogP 1.92 TPSA 61.4	✓ Ro5	✓ Clean	`O=C(NC1CCCCC1)NC1CCC(O)CC1`
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…`
ZINC4910418	0.739	225.3 Da LogP 1.37 TPSA 53.2	✓ Ro5	✓ Clean	`O=C(NC1CCCCC1)NC1CCNCC1`
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`
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](…`

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.