Protein target profile

VK055_3135

fatty oxidation complex, alpha subunit FadB

Genome: KpATCC43816 Gene: fadB AIK81707.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 5 reactions UniProt A0A0H3GPY7
Length 729
Pocket druggability 0.91
Metabolic reactions 5
Chokepoint No
Direct ligand evidence 0 58 total records
Functional annotation 0 EC 14 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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 (%)
42.742 Lower values reduce human off-target concern.
Human E-value
6.27e-25
Gut microbiome similarity
3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
55.804 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
95.55 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 0.91
Structure A0A0H3GPY7
Pocket Pocket 1
P2Rank 0.861
Structure A0A0H3GPY7
Pocket Pocket 1
ColabFold model
FPocket 0.919 · Pocket 1
P2Rank 0.822 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 143 / 4744 genomes with a hit
Prevalence 3.0%

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.

Explore metabolic network

Metabolic context: more central than 97.1% of genes in this genome.

Relative network centrality 97.1% more central than 97.1% of genes in this genome
Chokepoint Not a chokepoint
Catalyzed reactions

5 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MLYKGDTLYLDWLEDGIAELVFDAPGSVNKLDTATVASLGHALDVLEKQSDLKGLLLRSEKAAFIVGADITEFLSLFLVPEEQLSQWLHFANSVFNRLEDLPVPTISAVNGYALGGGCECVLATDYRLATPDLRIGLPETKLGIMPGFGGSVRLPRLLGADSALEIIAAGKDVGADQALKIGLVDGVVAAEKLRDGALAILRQAMNGDLDWKAKRQPKLEPLKLSKIEAAMSFTIAKGMVAQTAGKHYPAPITAVKTIEAAARLGREEALVLENKSFVPLAHTNEARALVGIFLNDQYVKAKAKKLTKDVETPKHAAVLGAGIMGGGIAYQSAWKGVPVVMKDISDKSLTLGMTEAAKLLNKQLERGKIDGLKLAGVISTIQPTLEYSGFDRVDVVVEAVVENPKVKKAVLAETEAKVRPDTVLASNTSTIPISELASVLQRPENFCGMHFFNPVHRMPLVEVIRGEKTSDNTIAKVVAWASKMGKTPIVVNDCPGFFVNRVLFPYFAGFSQLLRDGADFRKVDKVMEKQFGWPMGPAYLLDVVGIDTAHHAQAVMAAGFPQRMQKDYRDAIDALFDANRFGQKNGLGFWRYKDDSKGKPKKEEDAAVDSLLADVSQPKRDFSDEEIIARMMIPMVNEVVRCLEEGIIASPAEADMALVYGLGFPPFHGGAFRWLDTIGSAKYLDMAQQYQHLGPLYEVPAGLRDKARHNEAYYPQVEPARPVGALKTA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

14 GO

Gene Ontology (GO)

14
  • GO:0003857 Catalysis of the reaction: a (3S)-3-hydroxyacyl-CoA + NAD+ = a 3-oxoacyl-CoA + NADH + H+.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0006631 The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0008692 Catalysis of the reaction: (S)-3-hydroxybutanoyl-CoA = (R)-3-hydroxybutanoyl-CoA.
  • GO:0004300 Catalysis of the reaction: a 3-hydroxy-fatty acyl-CoA = a enoyl-CoA + H2O. This reaction usually occurs in the reverse direction, leading to the reduction of the double bound of enoyl-CoA in position 2 or 3. Specific reactions catalyzed include: a 4-saturated-(3S)-3-hydroxyacyl-CoA = a (3E)-enoyl-CoA + H2O and a (3S)-3-hydroxyacyl-CoA = a (2E)-enoyl-CoA + H2O.
  • GO:0036125 A multienzyme complex possessing three kinds of enzymes that catalyze the chain reactions in the fatty acid beta-oxidation cycle, enoyl-CoA hydratase (ECH), 3-hydroxyacyl-CoA dehydrogenase (HACD), and acetyl-CoA C-acyltransferase (KACT).
  • GO:0009062 The chemical reactions and pathways resulting in the breakdown of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
  • GO:0016616 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
  • GO:0070403 Binding to the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
  • GO:0004165 Catalysis of the reactions: a (3Z)-enoyl-CoA = a 4-saturated (2E)-enoyl-CoA or a (3E)-enoyl-CoA = a 4-saturated (2E)-enoyl-CoA.
  • GO:0018812 Catalysis of the reaction: a 3-hydroxy-fatty acyl-CoA = a (2E)-enoyl-CoA + H2O.
  • GO:0016509 Catalysis of the reaction: a long-chain (3S)-3-hydroxy fatty acyl-CoA + NAD+ = a long-chain 3-oxo-fatty acyl-CoA + H+ + NADH. A long-chain fatty acid has an aliphatic tail containing 13 to 22 carbons.
  • GO:0006635 A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A; the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
496 592 Pfam PF00725 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
496 592 InterPro IPR006108 3-hydroxyacyl-CoA dehydrogenase, C-terminal
627 691 Pfam PF00725 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
627 691 InterPro IPR006108 3-hydroxyacyl-CoA dehydrogenase, C-terminal
1 714 NCBIfam TIGR02437 fatty acid oxidation complex subunit alpha FadB
1 714 InterPro IPR012799 Fatty oxidation complex, alpha subunit FadB
1 312 FunFam G3DSA:3.90.226.10:FF:000018 Fatty acid oxidation complex subunit alpha
499 714 FunFam G3DSA:1.10.1040.50:FF:000001 Fatty acid oxidation complex subunit alpha
14 203 CDD cd06558 crotonase-like
1 715 Hamap MF_01621 Fatty acid oxidation complex subunit alpha [fadB].
1 715 InterPro IPR012799 Fatty oxidation complex, alpha subunit FadB
622 714 SUPERFAMILY SSF48179 6-phosphogluconate dehydrogenase C-terminal domain-like
622 714 InterPro IPR008927 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily
493 517 ProSitePatterns PS00067 3-hydroxyacyl-CoA dehydrogenase signature.
493 517 InterPro IPR006180 3-hydroxyacyl-CoA dehydrogenase, conserved site
106 126 ProSitePatterns PS00166 Enoyl-CoA hydratase/isomerase signature.
106 126 InterPro IPR018376 Enoyl-CoA hydratase/isomerase, conserved site
4 714 PANTHER PTHR43612 TRIFUNCTIONAL ENZYME SUBUNIT ALPHA
313 498 FunFam G3DSA:3.40.50.720:FF:000009 Fatty oxidation complex, alpha subunit
313 498 Gene3D G3DSA:3.40.50.720 -
314 495 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
314 495 InterPro IPR036291 NAD(P)-binding domain superfamily
316 494 Pfam PF02737 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
316 494 InterPro IPR006176 3-hydroxyacyl-CoA dehydrogenase, NAD binding
3 303 SUPERFAMILY SSF52096 ClpP/crotonase
3 303 InterPro IPR029045 ClpP/crotonase-like domain superfamily
1 312 Gene3D G3DSA:3.90.226.10 -
499 718 Gene3D G3DSA:1.10.1040.50 -
14 206 Pfam PF00378 Enoyl-CoA hydratase/isomerase
14 206 InterPro IPR001753 Enoyl-CoA hydratase/isomerase
495 638 SUPERFAMILY SSF48179 6-phosphogluconate dehydrogenase C-terminal domain-like
495 638 InterPro IPR008927 6-phosphogluconate dehydrogenase-like, C-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 #1
0.91
Likely same site as P2Rank 2 1.6 Å 21 shared residues 100% of smaller site
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Surrounding area
Site 2 FPocket #28
0.262
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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
0.861
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.795
Likely same site as FPocket 1 1.6 Å 21 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.515
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Surrounding area
Site 4 P2Rank #4
0.266
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Surrounding area
Site 5 P2Rank #5
0.056
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Surrounding area
Residue sets
UniProt: Active site:450-450 For 3-hydroxyacyl-CoA dehydrogenase activity
UniProt: Binding site:296-296
UniProt: Binding site:324-324
UniProt: Binding site:343-343
UniProt: Binding site:400-402
UniProt: Binding site:407-407
UniProt: Binding site:429-429
UniProt: Binding site:453-453
UniProt: Binding site:500-500
UniProt: Binding site:660-660
UniProt: Site:119-119 Important for catalytic activity
UniProt: Site:139-139 Important for catalytic activity
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_A0A0H3GPY7
AlphaFold DB full sequence Viewing
ColabFold VK055_3135
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.

58 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 8 records from similar proteins
Structural ligands 8 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
3H9 PDB via homolog 877.7 Da · LogP -3.31 · TPSA 395.2 Open detail RCSB PDB
3HC PDB via homolog Detail RCSB PDB
CAA PDB via homolog Detail RCSB PDB
HSC PDB via homolog Detail RCSB PDB
N8E 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
3H9 RCSB PDB P07896 877.7 Da LogP -3.31 TPSA 395.2 3 viol. ✓ Clean CCC[C@@H](CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)…
3HC RCSB PDB Q16836 853.6 Da LogP -1.56 TPSA 383.9 3 viol. ✓ Clean CC(CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@](…
CAA RCSB PDB C4IEM5 851.6 Da LogP -1.36 TPSA 380.7 3 viol. ✓ Clean CC(=O)CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P…
HSC RCSB PDB P07896 933.8 Da LogP -1.75 TPSA 395.2 3 viol. ✓ Clean CCCCCCC[C@@H](CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C…
N8E RCSB PDB P28793 350.5 Da LogP 2.42 TPSA 66.4 ✓ Ro5 ✓ Clean CCCCCCCCOCCOCCOCCOCCOCCO
T1G RCSB PDB P07896 863.6 Da LogP -3.85 TPSA 395.2 3 viol. ✓ Clean C[C@@H]([C@H](C)O)C(=O)SCCNC(=O)CCNC(=O)[C@@H](…
TC6 RCSB PDB P07896 859.6 Da LogP -2.51 TPSA 374.9 2 viol. ✓ Clean CCC/C=C/C(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP…
ZOZ RCSB PDB P07896 935.8 Da LogP 0.98 TPSA 380.7 3 viol. ✓ Clean CCCCCCCC(=O)CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(…

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.