Protein target profile

KP13_00022

ATP synthase subunit delta

Genome: KpKP13 Gene: AHE47131.1 atpH 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GXU5

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Length 177

Pocket druggability 0.66

Direct ligand evidence 0 5 total records

Functional annotation 0 EC 5 GO

Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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

Main supporting evidence

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Moderate predicted binding pocket FPocket selected-pocket score 0.66. This supports review but is not experimental validation. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 0 structural and 1 bioactivity records.

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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 (%): 24.118 Lower values reduce human off-target concern.
Human E-value: 2.5e-10
Gut microbiome similarity: 2.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 88.136 Higher values support similarity to known essential genes.
DEG E-value: 6.309999999999999e-115 Smaller values mean stronger essential-gene similarity.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 75.85 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 0.66

Structure A0A0H3GXU5

Pocket Pocket 3

P2Rank

Structure A0A0H3GXU5

Pocket No pockets

ColabFold model

FPocket 0.678 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 136 / 4744 genomes with a hit

Prevalence 2.9%

Cross-references

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

Sequence

UniProt A0A0H3GXU5

Chemistry

ChEMBL DWT

Sequence

Primary amino-acid sequence viewer.

MSEFVTVARPYAKAAFDFAVEHNSVERWQDMLAFAAEVTKNDQMAELLSGALAPETLSEAFIAICGEQLDENGQNLIKVMAENNRLKVLPDVLEQFIHLRAASEAIAEVEVISANQLSDEQLARIVSAMEKRLSRKVKLNCKIDKSVMAGIIIRAGDMVIDGSVRGRLERLADVLQS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
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: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.

25 records

Show feature table

Start	End	DB	Term	Name
74	85	PRINTS	PR00125	ATP synthase delta subunit signature
74	85	InterPro	IPR000711	ATPase, OSCP/delta subunit
85	99	PRINTS	PR00125	ATP synthase delta subunit signature
85	99	InterPro	IPR000711	ATPase, OSCP/delta subunit
7	26	PRINTS	PR00125	ATP synthase delta subunit signature
7	26	InterPro	IPR000711	ATPase, OSCP/delta subunit
150	168	PRINTS	PR00125	ATP synthase delta subunit signature
150	168	InterPro	IPR000711	ATPase, OSCP/delta subunit
135	150	PRINTS	PR00125	ATP synthase delta subunit signature
135	150	InterPro	IPR000711	ATPase, OSCP/delta subunit
3	177	Hamap	MF_01416	ATP synthase subunit delta [atpD].
3	177	InterPro	IPR000711	ATPase, OSCP/delta subunit
137	156	ProSitePatterns	PS00389	ATP synthase delta (OSCP) subunit signature.
137	156	InterPro	IPR020781	ATPase, OSCP/delta subunit, conserved site
2	106	FunFam	G3DSA:1.10.520.20:FF:000001	ATP synthase subunit delta
3	104	SUPERFAMILY	SSF47928	N-terminal domain of the delta subunit of the F1F0-ATP synthase
3	104	InterPro	IPR026015	F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily
7	175	NCBIfam	TIGR01145	ATP synthase F1 subunit delta
7	175	InterPro	IPR000711	ATPase, OSCP/delta subunit
7	174	Pfam	PF00213	ATP synthase delta (OSCP) subunit
7	174	InterPro	IPR000711	ATPase, OSCP/delta subunit
6	176	PANTHER	PTHR11910	ATP SYNTHASE DELTA CHAIN
6	176	InterPro	IPR000711	ATPase, OSCP/delta subunit
2	106	Gene3D	G3DSA:1.10.520.20	-
2	106	InterPro	IPR026015	F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily

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 #3

0.66

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Surrounding area

Site 2 FPocket #7

0.444

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Surrounding area

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_A0A0H3GXU5	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_00022	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.

5 records

Chemistry signal

Bioactivity evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 1 records from similar proteins

Structural ligands 0 0 loaded crystals

Measured bioactivity 1 direct and transferred ChEMBL records

Proposed compounds 4 similarity-based ZINC candidates

Best available ligand signal

DWT ChEMBL via homolog pchembl 7.69 (~20.4 nM) 503.5 Da · LogP 5.75 · TPSA 97.6 Open detail ChEMBL

ZINC220133900 ZINC proposed compound · Tanimoto 0.538 Detail ZINC

ZINC20148987 ZINC proposed compound · Tanimoto 0.532 Detail ZINC

ZINC9306398 ZINC proposed compound · Tanimoto 0.512 Detail ZINC

ZINC5049572 ZINC proposed compound · Tanimoto 0.507 Detail ZINC

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, 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.

No PDB ligands found through similar proteins.

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
DWT ChEMBL	P48047	7.69 ~20.4 nM	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cn(nc3nc(n2)c4cccnc4)C)C(=O)Nc5c…`

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
ZINC220133900 ZINC	0.538	398.3 Da LogP 3.77 TPSA 85.1	✓ Ro5	✓ Clean	`Cc1nc2nc(-c3cccnc3)nn2cc1C(=O)Nc1cccc(C(F)(F)F)…`
ZINC20148987 ZINC	0.532	414.4 Da LogP 4.50 TPSA 97.1	✓ Ro5	✓ Clean	`Cc1ccc(C(=O)Nc2cccc(C(F)(F)F)c2)cc1Nc1cncc(C(N)…`
ZINC9306398 ZINC	0.512	398.3 Da LogP 3.77 TPSA 85.1	✓ Ro5	✓ Clean	`Cc1c(C(=O)Nc2cccc(C(F)(F)F)c2)cnc2nc(-c3cccnc3)…`
ZINC5049572 ZINC	0.507	336.3 Da LogP 4.22 TPSA 58.2	✓ Ro5	✓ Clean	`CC(=O)Nc1cc(C(=O)Nc2cccc(C(F)(F)F)c2)ccc1C`

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.