Protein target profile

KP13_05088

Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B

Genome: KpKP13 Gene: lpsJ AHE44206.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GPA6
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Length 218
Pocket druggability 0.415
Functional annotation 0 EC 1 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 0.41. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.70. Structure available AlphaFold DB model + ColabFold model

Risks to review

Human similarity Top human hit identity: 49.767%. This target also has a predicted binding pocket (FPocket 0.41) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 252 of 4744 screened genomes (5.3%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.41) — check the ligand evidence before deprioritizing on off-target risk alone.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. No ligand evidence No experimental PDB ligands, measured ChEMBL bioactivity, or proposed ZINC compound records are available.
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 (%)
49.767 Lower values reduce human off-target concern.
Human E-value
2.59e-69
Gut microbiome similarity
5.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
51.835 Higher values support similarity to known essential genes.
DEG E-value
1.21e-77 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.27 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 0.415
Structure A0A0H3GPA6
Pocket Pocket 7
P2Rank 0.699
Structure A0A0H3GPA6
Pocket Pocket 1
ColabFold model
FPocket 0.222 · Pocket 6
P2Rank 0.657 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 252 / 4744 genomes with a hit
Prevalence 5.3%

Cross-references

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

Sequence

UniProt A0A0H3GPA6

Sequence

Primary amino-acid sequence viewer.

MLTREQMAMRVAQELRDGDYVNLGIGIPTLVANYIPAGIEVMLQSENGLLGMGEFPDEETIDADMINAGKQTVTAQTGAAIFDSAQSFAMIRGGHVDLTVLGAFEVDVAGNIASWMIPGKMVKGMGGAMDLVAGAQNIIVVMTHASKNGESKLLPQCTLPLTGVGCIRRVLTDLALLEIVDGAFVLREVAPGVSPDEVIRKTAGRLIVADDVREMRFS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

1
  • GO:0008410 Catalysis of the transfer of a coenzyme A (CoA) group from one compound (donor) to another (acceptor).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
3 216 PANTHER PTHR13707 KETOACID-COENZYME A TRANSFERASE
3 216 InterPro IPR004165 Coenzyme A transferase family I
1 213 FunFam G3DSA:3.40.1080.10:FF:000001 Succinyl-coa:3-ketoacid-coenzyme a transferase subunit b
3 216 SUPERFAMILY SSF100950 NagB/RpiA/CoA transferase-like
3 216 InterPro IPR037171 NagB/RpiA transferase-like
21 43 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
5 200 Pfam PF01144 Coenzyme A transferase
5 200 InterPro IPR004165 Coenzyme A transferase family I
43 51 ProSitePatterns PS01274 Coenzyme A transferases signature 2.
43 51 InterPro IPR004164 Coenzyme A transferase active site
1 213 Gene3D G3DSA:3.40.1080.10 -
5 201 SMART SM00882 CoA_trans_3
5 201 InterPro IPR004165 Coenzyme A transferase family I
3 207 NCBIfam TIGR02428 3-oxoacid CoA-transferase subunit B
3 207 InterPro IPR012791 3-oxoacid CoA-transferase, subunit B

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 #7
0.415
Likely same site as P2Rank 2 2.0 Å 9 shared residues 90% of smaller site
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Surrounding area
Site 2 FPocket #10
0.22
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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
0.699
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Surrounding area
Site 2 P2Rank #2
0.051
Likely same site as FPocket 7 2.0 Å 9 shared residues 90% of smaller site
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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_A0A0H3GPA6
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_05088
ColabFold — — full sequence — Loaded