Protein target profile

KP13_02931

Acyl-coenzyme A dehydrogenase

Genome: KpKP13 Gene: fadE AHE46204.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GS96

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Length 814

Pocket druggability 0.998

Direct ligand evidence 0 10 total records

Functional annotation 2 EC 7 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.

Main supporting evidence

Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 1.00, P2Rank 0.96). Use the 3D pocket comparison to verify whether they identify the same site. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 1.00. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.96. Review the complete evidence below

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 (%): 31.606 Lower values reduce human off-target concern.
Human E-value: 3.92e-14
Gut microbiome similarity: 2.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 0.0 Higher values support similarity to known essential genes.

Localization

Localization: CytoplasmicMembrane

Structure confidence

ColabFold pLDDT: 93.38 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 0.998

Structure A0A0H3GS96

Pocket Pocket 4

P2Rank 0.959

Structure A0A0H3GS96

Pocket Pocket 1

ColabFold model

FPocket 0.989 · Pocket 1

P2Rank 0.967 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 137 / 4744 genomes with a hit

Prevalence 2.9%

Cross-references

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

Sequence

UniProt A0A0H3GS96

Sequence

Primary amino-acid sequence viewer.

MMILSIVATVVLLGALFYHRVSLLLSSVILLAWTAALGAAGVWNIWLLLPLAIILLPFNFAPMRKSMISAPAFRTFRKVMPPMSRTEKEAIDAGTTWWEGDLFRGNPDWQKLHNYPQPRLTAEEQAFLDGPVEEACRMANDFAITHEMADLPPELWAYLKEHRFFAMIIKKEYGGLEFSAYAQARVLQKLSGVSGILAITVGVPNSLGPGELLQHYGTEEQKNHYLPRLARGLEIPCFALTSPEAGSDAGAIPDTGVVCMGDWQGQQVLGMRLTWNKRYITLAPIATVLGLAFKLSDPDRLLGGEEELGITCALIPTSTPGVEIGRRHFPLNVPFQNGPTRGKDIFVPIDYIIGGPSMAGQGWRMLVECLSVGRGITLPSNATGGLKSVAMATGAYAHIRRQFKISIGKMEGIEEALARIAGNAYVMDAAASLITYGIMLGEKPAVLSAIVKYHCTHRGQRSIIDAMDITGGKGIMLGEGNFLARAYQGAPIAITVEGANILTRSMMIFGQGAIRCHPYVLEEMAAAQNNDLNAYDKLLFKHIGHVGSNKVRSFWLGLTGGRTSSAPTRDATRRYYQQMNRLSANLALLSDVSMAVLGGSLKRRERISARLGDVLSQLYLASAVLKRYDDEGRNEADLPLVHWGVQDALHQAEQAIDDLLDNFPNRLVAGVMRLVIFPTGRHHHAPSDRLDHQVAKILQVPSATRSRIGRGQYLTPSEHNPVGLLEEALLEVMAADPIHQRICKELGKNLPFTRLDELAHNALAKGLISQDEAAILTRAEHSRLRSINVDDFAPEELATKPVKLPEKVRKVEAA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 7 GO

Enzyme Commission (EC)

Gene Ontology (GO)

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.
GO:0033539 A fatty acid beta-oxidation pathway in which the initial step of each oxidation cycle, which converts an acyl-CoA to a trans-2-enoyl-CoA, is catalyzed by acyl-CoA dehydrogenase; the electrons removed by oxidation pass through the respiratory chain to oxygen and leave H2O as the product. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0004466 Catalysis of the reaction: a long-chain 2,3-saturated fatty acyl-CoA + H+ + oxidized [electron-transfer flavoprotein] = a long-chain (2E)-enoyl-CoA + reduced [electron-transfer flavoprotein]. A long-chain fatty acid has an aliphatic tail containing 13 to 22 carbons.
GO:0070991 Catalysis of the reaction: a medium-chain 2,3-saturated fatty acyl-CoA + H+ + oxidized [electron-transfer flavoprotein] = a medium-chain trans-(2E)-enoyl-CoA + reduced [electron-transfer flavoprotein]. A medium-chain fatty acid has an aliphatic tail containing 6 to 12 carbons.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

34 records

Show feature table

Start	End	DB	Term	Name
582	601	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
360	506	FunFam	G3DSA:1.20.140.10:FF:000009	Acyl-CoA dehydrogenase
120	235	Gene3D	G3DSA:1.10.540.10	-
120	235	InterPro	IPR037069	Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily
236	359	Gene3D	G3DSA:2.40.110.10	-
236	359	InterPro	IPR046373	Acyl-CoA oxidase/dehydrogenase, middle domain superfamily
27	35	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	3	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
514	792	Pfam	PF09317	Acyl-CoA dehydrogenase, C-terminal, bacterial type
514	792	InterPro	IPR015396	Acyl-CoA dehydrogenase, C-terminal, bacterial-type
10	32	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
3	814	NCBIfam	NF038187	acyl-CoA dehydrogenase FadE
3	814	InterPro	IPR047634	Acyl-CoA dehydrogenase FadE
360	506	Gene3D	G3DSA:1.20.140.10	-
236	359	FunFam	G3DSA:2.40.110.10:FF:000010	Acyl-CoA dehydrogenase
39	61	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
360	504	Pfam	PF00441	Acyl-CoA dehydrogenase, C-terminal domain
360	504	InterPro	IPR009075	Acyl-CoA dehydrogenase/oxidase C-terminal
4	17	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
602	814	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
36	58	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
119	235	FunFam	G3DSA:1.10.540.10:FF:000004	Acyl-CoA dehydrogenase
1	26	Phobius	SIGNAL_PEPTIDE	Signal peptide region
135	232	Pfam	PF02771	Acyl-CoA dehydrogenase, N-terminal domain
135	232	InterPro	IPR013786	Acyl-CoA dehydrogenase/oxidase, N-terminal
237	328	Pfam	PF02770	Acyl-CoA dehydrogenase, middle domain
237	328	InterPro	IPR006091	Acyl-CoA oxidase/dehydrogenase, middle domain
360	515	SUPERFAMILY	SSF47203	Acyl-CoA dehydrogenase C-terminal domain-like
360	515	InterPro	IPR036250	Acyl-CoA dehydrogenase-like, C-terminal
76	505	PANTHER	PTHR48083	MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL-RELATED
117	355	SUPERFAMILY	SSF56645	Acyl-CoA dehydrogenase NM domain-like
117	355	InterPro	IPR009100	Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily
18	26	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
59	581	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.

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 #4

0.998

Likely same site as P2Rank 2 5.6 Å 23 shared residues 79% of smaller site

Unusual size

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Surrounding area

Site 2 FPocket #1

0.947

Unusual size

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Surrounding area

Site 3 FPocket #50

0.939

Unusual size

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Surrounding area

Site 4 FPocket #47

0.55

Likely same site as P2Rank 3 3.5 Å 13 shared residues 87% of smaller site

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

0.959

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Surrounding area

Site 2 P2Rank #2

0.901

Likely same site as FPocket 4 5.6 Å 23 shared residues 79% of smaller site

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Surrounding area

Site 3 P2Rank #3

0.517

Likely same site as FPocket 47 3.5 Å 13 shared residues 87% of smaller site

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Surrounding area

Site 4 P2Rank #4

0.479

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Surrounding area

Site 5 P2Rank #5

0.443

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Surrounding area

Binding pockets · FPocket

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

Site 1 FPocket #1

0.989

Likely same site as P2Rank 1 5.9 Å 40 shared residues 83% of smaller site

Unusual size

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Surrounding area

Site 2 FPocket #44

0.984

Unusual size

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Surrounding area

Site 3 FPocket #3

0.866

Likely same site as P2Rank 2 5.0 Å 15 shared residues 83% of smaller site

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Surrounding area

Site 4 FPocket #18

0.572

Likely same site as P2Rank 3 2.0 Å 15 shared residues 94% of smaller site

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

0.967

Likely same site as FPocket 1 5.9 Å 40 shared residues 83% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.869

Likely same site as FPocket 3 5.0 Å 15 shared residues 83% of smaller site

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Surrounding area

Site 3 P2Rank #3

0.626

Likely same site as FPocket 18 2.0 Å 15 shared residues 94% of smaller site

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Surrounding area

Site 4 P2Rank #4

0.427

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Surrounding area

Site 5 P2Rank #5

0.392

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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_A0A0H3GS96	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_02931	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.

10 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 5 records from similar proteins

Structural ligands 5 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 5 similarity-based ZINC candidates

Best available ligand signal

CAA PDB via homolog 851.6 Da · LogP -1.36 · TPSA 380.7 Open detail RCSB PDB

COS PDB via homolog Detail RCSB PDB

FDA PDB via homolog Detail RCSB PDB

MYA PDB via homolog Detail RCSB PDB

TH3 PDB via homolog Detail RCSB PDB

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CAA RCSB PDB	1JQI	P15651	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…`
COS RCSB PDB	4L1F	D2RL84	799.6 Da LogP -1.02 TPSA 346.6	3 viol.	✓ Clean	`CC(C)(CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([…`
FDA RCSB PDB	4N5F	B4EGC8	787.6 Da LogP -1.75 TPSA 363.3	3 viol.	✓ Clean	`Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C…`
MYA RCSB PDB	3B96	P49748	977.9 Da LogP 3.37 TPSA 363.6	3 viol.	✓ Clean	`CCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(…`
TH3 RCSB PDB	2UXW	P49748	1003.9 Da LogP 3.92 TPSA 363.6	3 viol.	✓ Clean	`CCCCCCCCCCCCC/C=C/C(=O)SCCNC(=O)CCNC(=O)C(C(C)(…`

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).

No ChEMBL hits found through similar proteins.

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
ZINC8586020 ZINC	0.522	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC12501123 ZINC	0.516	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC4228234 ZINC	0.516	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC79671662 ZINC	0.516	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC79671663 ZINC	0.516	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](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.