Genome KpATCC43816

Protein target profile

aidB

Accession: VK055_2882

Gene: AIK81472.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GH98
Length 545
Pocket druggability (P2Rank) 0.932
Direct ligand evidence 0 65 total records
Functional annotation 0 EC 2 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 (%)
29.67 Lower values reduce human off-target concern.
Human E-value
5.25e-14
Gut microbiome similarity
2.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
46.018 Higher values support similarity to known essential genes.
DEG E-value
2.27e-131 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
96.64 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.932
Structure A0A0H3GH98
Pocket Pocket 1
Druggability (FPocket) 0.981
Structure A0A0H3GH98
Pocket Pocket 1
ColabFold model
P2Rank 0.937 · Pocket 1
FPocket 0.952 · Pocket 3
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 95 / 4744 genomes with a hit
Prevalence 2.0%

Cross-references

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

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MHWQTHTVFNQPTPLNNSNLFLSDTALREAVVREGAGWDGDLLASIGQQLGTAESLELGRLANSNPPELLRYDATGARLDDVRFHPAWHLLMQGLCANRVHNLAWQEDAREGAFVARAARFLLHAQVEAGTLCPITMTFAATPLLQHALPAPFRDWLSPLLSDRYDPHLAPGGQKRGLLIGMGMTEKQGGSDVLSNTTRAEKTAEGFYRLVGHKWFFSVPQSDAHLVLAQAPTGLSCFFVPRLLPDGQRNGVRLERLKEKLGNRSNASSEVEFYEACGWLVGDEGDGVRQILRMGGLTRFDCALGSHALMRRAFSVALYHALQRQAFGKNLVEQPMMRQLLGQMALRLEGQTAFLFRLARAWDRRDDARESAWARLFTPAAKFAICKAGIPFVAEAMEVLGGIGYCEESELPRLYREMPVNSIWEGSGNIMCLDVMRVLSKQPAAMELLAAECAEVKGQNRHLNRAWRQLQQLLKRPAEEQGREIARLVYRLGAGAQMLRHASPPLAEAWCRMMLDTRGGIRLDAPTLDDLLLRAMGRGRQAPQA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

2
  • GO:0003995 Catalysis of the reaction: a 2,3-saturated acyl-CoA + H+ oxidized [electron-transfer flavoprotein] = a (2E)-enoyl-CoA + reduced [electron-transfer flavoprotein].
  • GO:0016627 Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
80 293 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like
80 293 InterPro IPR009100 Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily
283 443 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like
283 443 InterPro IPR036250 Acyl-CoA dehydrogenase-like, C-terminal
183 195 ProSitePatterns PS00072 Acyl-CoA dehydrogenases signature 1.
183 195 InterPro IPR006089 Acyl-CoA dehydrogenase, conserved site
286 465 Gene3D G3DSA:1.20.140.10 -
130 285 Gene3D G3DSA:2.40.110.20 -
3 518 PANTHER PTHR42707 ACYL-COA DEHYDROGENASE
181 273 Pfam PF02770 Acyl-CoA dehydrogenase, middle domain
181 273 InterPro IPR006091 Acyl-CoA oxidase/dehydrogenase, middle domain
10 167 Pfam PF18158 Adaptive response protein AidB N-terminal domain
10 167 InterPro IPR041504 Adaptive response protein AidB, N-terminal
398 417 ProSitePatterns PS00073 Acyl-CoA dehydrogenases signature 2.
398 417 InterPro IPR006089 Acyl-CoA dehydrogenase, conserved site
285 439 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain
285 439 InterPro IPR009075 Acyl-CoA dehydrogenase/oxidase C-terminal
52 105 Gene3D G3DSA:6.10.250.600 -

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.

Download VMD script Full viewer

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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 · P2Rank

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

Pocket 1 P2Rank #1
0.932
Likely same site as FPocket 1 1.5 Å 32 shared residues 97% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.151
Likely same site as FPocket 39 2.0 Å 9 shared residues 82% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.118
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Surrounding area
Pocket 4 P2Rank #4
0.104
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Surrounding area
Pocket 5 P2Rank #5
0.104
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.981 Unusual size
Likely same site as P2Rank 1 1.5 Å 32 shared residues 97% of smaller site
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Surrounding area
Pocket 2 FPocket #36
0.396
Show in viewer
Surrounding area
Pocket 3 FPocket #22
0.234
Show in viewer
Surrounding area
Pocket 4 FPocket #39
0.21
Likely same site as P2Rank 2 2.0 Å 9 shared residues 82% of smaller site
Show in viewer
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_A0A0H3GH98
AlphaFold DB full sequence Viewing
ColabFold VK055_2882
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.

65 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 15 records from similar proteins
Structural ligands 15 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
6NA PDB via homolog 116.2 Da · LogP 1.65 · TPSA 37.3 Open detail RCSB PDB
B3P PDB via homolog Detail RCSB PDB
BUA PDB via homolog Detail RCSB PDB
CAC PDB via homolog Detail RCSB PDB
DAO 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
6NA RCSB PDB Q3L887 116.2 Da LogP 1.65 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCC(=O)O
B3P RCSB PDB A3SI50 282.3 Da LogP -4.01 TPSA 145.4 1 viol. ✓ Clean C(CNC(CO)(CO)CO)CNC(CO)(CO)CO
BUA RCSB PDB Q3L887 88.1 Da LogP 0.87 TPSA 37.3 ✓ Ro5 ✓ Clean CCCC(=O)O
CAC RCSB PDB Q8YC61 137.0 Da LogP -0.52 TPSA 40.1 ✓ Ro5 ✓ Clean C[As](=O)(C)[O-]
DAO RCSB PDB Q3L887 200.3 Da LogP 3.99 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCCCCCC(=O)O
DCR RCSB PDB Q3L887 312.5 Da LogP 7.11 TPSA 37.3 1 viol. ✓ Clean CCCCCCCCCCCCCCCCCCCC(=O)O
DKA RCSB PDB Q3L887 172.3 Da LogP 3.21 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCCCC(=O)O
EO3 RCSB PDB Q3L887 340.6 Da LogP 7.89 TPSA 37.3 1 viol. ✓ Clean CCCCCCCCCCCCCCCCCCCCCC(=O)O
MFK RCSB PDB Q6MJ59 921.8 Da LogP 1.81 TPSA 363.6 3 viol. ✓ Clean CCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO…
MYR RCSB PDB Q3L887 228.4 Da LogP 4.77 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCCCCCCCC(=O)O
OCA RCSB PDB Q3L887 144.2 Da LogP 2.43 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCC(=O)O
PLM RCSB PDB Q3L887 256.4 Da LogP 5.55 TPSA 37.3 1 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)O
ST9 RCSB PDB Q3L887 1034.0 Da LogP 4.93 TPSA 363.6 3 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C…
UCC RCSB PDB Q9XWZ2 935.8 Da LogP 2.20 TPSA 363.6 3 viol. ✓ Clean CCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)C…
X90 RCSB PDB Q3L887 270.5 Da LogP 5.94 TPSA 37.3 1 viol. ✓ Clean CCCCCCCCCCCCCCCCC(=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.