Protein target profile

PA4995

acyl-CoA dehydrogenase

Genome: NC_002516.2

Gene: PA4995 3D evidence: AlphaFold DB model UniProt Q9HUH0

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Length 429

Pocket druggability 0.713

Ligand records 18

EC / GO 1 / 5

Target summary

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

4 signals

How to read 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 TPW 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.

Overview

Basic information about this protein and its source genome.

Accession: PA4995
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA4995
Status: annotated
Amino acids: 429
3D evidence: AlphaFold DB model

3.13.1.4

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. 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: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: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: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.

Target profile

Computed evidence for target prioritization.

Human off-target: Hit
Human identity (%): 35.417
Human E-value: 4.75e-09
Gut microbiome off-target: Hit
Essential (DEG): Y
Localization: Cytoplasmic

Selected pocket evidence

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 0.713

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MPMSTDVQGRALAVLNRVAQADWPDRFNLRKPFEKLLYSGSRTGFRLASERSAKQAKGPRKADPDGLFDLSFSDDQQMLVDMLEGFALEVLRPLAHDADAEASLPAELLNQALELGLTHYGVGEVHGGMAGERTTVTTALIAEALAKGDLTLAAALLVPLSAANCIRRWGSPSQQAQWLPAFVSEEGAPLTAIAVNEPSLLFDPQKLATRARRKGSHYLLSGEKCLVLRGLEASRLIVAAKTDEGPALFLVEASAKGVERRAEPAMGLKAGGTARLRLKSVKVPADNRLAAEHFDYRAFLDHASLAWCALALGTGQAALDYVIAYCNEREAFGEPISHRQGVAFMVADIAIELDAMRLMVWRACALAERGQPFQREAYLARLLCAEKAMKIGTDAVQLLGGHGFTKEHPAERWYRDLRAVALMAGGLHL

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

3.13.1.4

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
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: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: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: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 Features

Domain/signature hits from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
191	297	Gene3D	G3DSA:2.40.110.10	-
191	297	InterPro	IPR046373	Acyl-CoA oxidase/dehydrogenase, middle domain superfamily
299	425	Pfam	PF00441	Acyl-CoA dehydrogenase, C-terminal domain
299	425	InterPro	IPR009075	Acyl-CoA dehydrogenase/oxidase C-terminal
297	428	FunFam	G3DSA:1.20.140.10:FF:000004	Acyl-CoA dehydrogenase FadE25
71	425	PANTHER	PTHR43884	ACYL-COA DEHYDROGENASE
192	281	Pfam	PF02770	Acyl-CoA dehydrogenase, middle domain
192	281	InterPro	IPR006091	Acyl-CoA oxidase/dehydrogenase, middle domain
68	290	SUPERFAMILY	SSF56645	Acyl-CoA dehydrogenase NM domain-like
68	290	InterPro	IPR009100	Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily
65	186	Gene3D	G3DSA:1.10.540.10	-
65	186	InterPro	IPR037069	Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily
73	186	Pfam	PF02771	Acyl-CoA dehydrogenase, N-terminal domain
73	186	InterPro	IPR013786	Acyl-CoA dehydrogenase/oxidase, N-terminal
397	416	ProSitePatterns	PS00073	Acyl-CoA dehydrogenases signature 2.
397	416	InterPro	IPR006089	Acyl-CoA dehydrogenase, conserved site
298	425	SUPERFAMILY	SSF47203	Acyl-CoA dehydrogenase C-terminal domain-like
298	425	InterPro	IPR036250	Acyl-CoA dehydrogenase-like, C-terminal
298	428	Gene3D	G3DSA:1.20.140.10	-

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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Structural evidence

0 + 1

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 PA4995	AlphaFold DB	—	—	full sequence	—	Viewing

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

0.713

Show in viewer

Site 2 FPocket #2

0.459

Show in viewer

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.

18 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 18 via homologs

Structural ligands 3 0 loaded crystals

Bioactive compounds 0 15 ZINC proposed compounds

Drug-like & clean 0 0 PAINS alerts

Best available ligand signal

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

Detail RCSB PDB CAA PDB via homolog

Detail RCSB PDB COS PDB via homolog

Detail RCSB PDB FDA PDB via homolog

Detail ZINC ZINC4228234 ZINC proposed compound · Tanimoto 0.573

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, 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	5OL2	A0A031WJ47	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	3PFD	G7CNE7	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…`

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
ZINC4228234 ZINC	0.573	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC12501123 ZINC	0.540	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	0.540	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	0.540	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…`
ZINC12360002 ZINC	0.500	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12360703 ZINC	0.500	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12503599 ZINC	0.500	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC16546165 ZINC	0.500	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…`
ZINC31977053 ZINC	0.500	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC4806433 ZINC	0.500	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC53683898 ZINC	0.500	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019 ZINC	0.500	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC8586020 ZINC	0.500	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021 ZINC	0.500	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC8586022 ZINC	0.500	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`

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.