Protein target profile

KP13_00025

ATP synthase subunit beta

Genome: KpKP13 Gene: AHE47134.1 atpD 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GVB4
Length 435
Pocket druggability 0.523
Direct ligand evidence 0 63 total records
Functional annotation 1 EC 9 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
Hit
Human identity (%)
71.493 Lower values reduce human off-target concern.
Human E-value
0.0
Gut microbiome similarity
69.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
98.161 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
93.67 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.523
Structure A0A0H3GVB4
Pocket Pocket 25
P2Rank 0.615
Structure A0A0H3GVB4
Pocket Pocket 1
ColabFold model
FPocket 0.869 · Pocket 14
P2Rank 0.66 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 3309 / 4744 genomes with a hit
Prevalence 69.8%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

Primary amino-acid sequence viewer.

MYEALEVQNGNEVLVLEVQQQLGGGIVRTIAMGSSDGLRRGLDVKDLEHPIEVPVGKATLGRIMNVLGQPVDMKGDIGEEERWAIHRAAPSYEELSSSQELLETGIKVIDLMCPFAKGGKVGLFGGAGVGKTVNMMELIRNIAIEHSGYSVFAGVGERTREGNDFYHEMTDSNVIDKVSLVYGQMNEPPGNRLRVALTGLTMAEKFRDEGRDVLLFVDNIYRYTLAGTEVSALLGRMPSAVGYQPTLAEEMGVLQERITSTKTGSITSVQAVYVPADDLTDPSPATTFAHLDATVVLSRQIASLGIYPAVDPLDSTSRQLDPLVVGQEHYDTARGVQSILQRYQELKDIIAILGMDELSEEDKLVVARARKIQRFLSQPFFVAEVFTGSPGKYVALKDTIRGFKGIMEGEYDHLPEQAFYMVGSIDEAVEKAKKL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • 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:0046034 The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:1902600 The directed movement of a proton across a membrane.
  • 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:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • 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: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: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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
52 323 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
52 323 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
117 302 SMART SM00382 AAA_5
117 302 InterPro IPR003593 AAA+ ATPase domain
4 50 SUPERFAMILY SSF50615 N-terminal domain of alpha and beta subunits of F1 ATP synthase
4 50 InterPro IPR036121 ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily
320 435 Gene3D G3DSA:1.10.1140.10 -
320 435 InterPro IPR024034 ATPase, F1/V1 complex, beta/alpha subunit, C-terminal
1 47 Pfam PF02874 ATP synthase alpha/beta family, beta-barrel domain
1 47 InterPro IPR004100 ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain
1 435 Hamap MF_01347 ATP synthase subunit beta [atpB].
1 435 InterPro IPR005722 ATP synthase, F1 complex, beta subunit
105 317 Pfam PF00006 ATP synthase alpha/beta family, nucleotide-binding domain
105 317 InterPro IPR000194 ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain
51 319 Gene3D G3DSA:3.40.50.300 -
51 319 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
308 317 ProSitePatterns PS00152 ATP synthase alpha and beta subunits signature.
308 317 InterPro IPR020003 ATPase, alpha/beta subunit, nucleotide-binding domain, active site
320 434 SUPERFAMILY SSF47917 C-terminal domain of alpha and beta subunits of F1 ATP synthase
1 435 NCBIfam TIGR01039 F0F1 ATP synthase subunit beta
324 431 CDD cd18110 ATP-synt_F1_beta_C
320 435 FunFam G3DSA:1.10.1140.10:FF:000001 ATP synthase subunit beta
52 322 CDD cd01133 F1-ATPase_beta_CD
51 319 FunFam G3DSA:3.40.50.300:FF:000004 ATP synthase subunit beta
1 50 Gene3D G3DSA:2.40.10.170 -
2 435 PANTHER PTHR15184 ATP SYNTHASE

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #25
0.523
Likely same site as P2Rank 2 0.9 Å 11 shared residues 100% of smaller site
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Surrounding area
Site 2 FPocket #4
0.225
Unusual size
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.615
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Surrounding area
Site 2 P2Rank #2
0.283
Likely same site as FPocket 25 0.9 Å 11 shared residues 100% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.246
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Surrounding area
Site 4 P2Rank #4
0.214
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Surrounding area
Site 5 P2Rank #5
0.139
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Surrounding area
Residue sets
UniProt: Binding site:150-157
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GVB4
AlphaFold DB full sequence Viewing
ColabFold KP13_00025
ColabFold full sequence Loaded

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.

63 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 13 records from similar proteins
Structural ligands 12 0 loaded crystals
Measured bioactivity 1 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
AF3 PDB via homolog 84.0 Da · LogP 0.88 · TPSA 0.0 Open detail RCSB PDB
ALF PDB via homolog Detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
AUR PDB via homolog Detail RCSB PDB
AZI PDB via homolog Detail RCSB PDB

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
AF3 RCSB PDB P00829 84.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean F[Al](F)F
ALF RCSB PDB P00829 103.0 Da LogP 1.30 TPSA 0.0 ✓ Ro5 ✓ Clean F[Al-](F)(F)F
ANP RCSB PDB P0ABB4 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 RCSB PDB 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 RCSB PDB P00829 42.0 Da LogP 0.87 TPSA 58.7 ✓ Ro5 Alert [N-]=[N+]=[N-]
BEF RCSB PDB P00829 66.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean [Be-](F)(F)F
DCW RCSB PDB P00829 224.3 Da LogP 2.95 TPSA 41.1 ✓ Ro5 ✓ Clean C1CCC(CC1)NC(=O)NC2CCCCC2
QUE RCSB PDB 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 RCSB PDB P00829 228.2 Da LogP 2.97 TPSA 60.7 ✓ Ro5 ✓ Clean c1cc(ccc1\C=C\c2cc(cc(c2)O)O)O
TS6 RCSB PDB P00829 114.1 Da LogP 0.01 TPSA 57.5 ✓ Ro5 ✓ Clean OP(=O)(O)S
TTX RCSB PDB P00825 414.5 Da LogP 0.99 TPSA 98.8 ✓ Ro5 ✓ Clean C[C@H]1C(=O)N[C@H](C(=O)N(/C(=C\c2ccccc2)/C(=O)…
VO4 RCSB PDB P10719 114.9 Da LogP -3.69 TPSA 86.2 ✓ Ro5 ✓ Clean [O-][V](=O)([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.