Protein target profile

PA2355

FMNH2-dependent monooxygenase

Genome: NC_002516.2

Gene: PA2355 3D evidence: AlphaFold DB model UniProt Q9I1C3
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Length 394
Pocket druggability 0.722
Ligand records 56
EC / GO 0 / 5
Target summary

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

4 signals

Strengths

Strong predicted binding pocket FPocket selected-pocket score 0.72. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model Ligand evidence via structure/bioactivity 6 structural and 0 bioactivity records.

Risks / watch

Human similarity Top human hit identity: 25.326%.

Missing evidence

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.
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
PA2355
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA2355
Status
annotated
Amino acids
394
3D evidence
AlphaFold DB model
GO
GO:0008470 Catalysis of the reaction: 3-methylbutanoyl-CoA + H+ + oxidized [electron-transfer flavoprotein] = 3-methyl-(2E)-butenoyl-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:0004497 Catalysis of the incorporation of one atom of molecular oxygen (O2) into the substrate and the reduction of the other atom of O2 to water. GO:0006552 The chemical reactions and pathways resulting in the breakdown of L-leucine. 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 (%)
25.326
Human E-value
1.13e-13
Gut microbiome off-target
Hit
Essential (DEG)
N
Localization
Unknown

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 0.722
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MNAKTRPEAQTPLQIARRLAADFAENAAERDVAGGTPKAERDALRRSGLLSLIIPREYGGLGASWSETLQTVRELARVDSSIAHVYGFQHLMLATVRLFSRPEQWQPWFELTARNRWFWGNALNPLDNRTVARRFDGWREFSGKKSFCSGARDSEMLIASALDGEGGALLIAAIPTARSGISLGQDWDNMGQRQTDSGSAIFERVRVEESELLLDPGPLSTPFACLRPLIAQLIFTEVFLGIAEGAFEEARQYTLREARPWFRSEVAEANADPYVLARYGEFWVGLESTRALVERAAQRLDAAWSKGPALDASERGQLALAIAAAKVAATRNGLDLCNRMFEVTGARSTHAALRLDRYWRNLRTQTLHDPLDYKIRELGDWALNQSPPQPTFYS

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0008470 Catalysis of the reaction: 3-methylbutanoyl-CoA + H+ + oxidized [electron-transfer flavoprotein] = 3-methyl-(2E)-butenoyl-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:0004497 Catalysis of the incorporation of one atom of molecular oxygen (O2) into the substrate and the reduction of the other atom of O2 to water.
  • GO:0006552 The chemical reactions and pathways resulting in the breakdown of L-leucine.
  • 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.

16 records
Show feature table
Start End DB Term Name
1 392 PIRSF PIRSF016578 PIGM
120 215 FunFam G3DSA:2.40.110.10:FF:000020 Putative acyl-CoA dehydrogenase YdbM
14 113 Pfam PF02771 Acyl-CoA dehydrogenase, N-terminal domain
14 113 InterPro IPR013786 Acyl-CoA dehydrogenase/oxidase, N-terminal
222 394 Gene3D G3DSA:1.20.140.10 -
120 216 Gene3D G3DSA:2.40.110.10 -
120 216 InterPro IPR046373 Acyl-CoA oxidase/dehydrogenase, middle domain superfamily
1 215 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like
1 215 InterPro IPR009100 Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily
234 369 Pfam PF08028 Acyl-CoA dehydrogenase, C-terminal domain
234 369 InterPro IPR013107 Acyl-CoA dehydrogenase, C-terminal domain
1 118 Gene3D G3DSA:1.10.540.10 -
1 118 InterPro IPR037069 Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily
17 368 PANTHER PTHR43884 ACYL-COA DEHYDROGENASE
234 390 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like
234 390 InterPro IPR036250 Acyl-CoA dehydrogenase-like, C-terminal

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.

3D visualization script Full viewer

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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 PA2355
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
0.722
Show in viewer
Site 2 FPocket #2
0.54
Show in viewer
Site 3 FPocket #3
0.305
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.

56 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 56 via homologs
Structural ligands 6 0 loaded crystals
Bioactive compounds 0 50 ZINC proposed compounds
Drug-like & clean 45 3 PAINS alerts
Best available ligand signal
83R PDB via homolog 184.3 Da · LogP 4.05 · TPSA 0.0 Open detail RCSB PDB
Detail RCSB PDB 83R PDB via homolog
Detail RCSB PDB 83U PDB via homolog
Detail RCSB PDB CAA PDB via homolog
Detail RCSB PDB COS PDB via homolog

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
83R RCSB PDB
5XDE
Q9LBX2 184.3 Da LogP 4.05 TPSA 0.0 ✓ Ro5 ✓ Clean c1ccc2c(c1)c3ccccc3s2
83U RCSB PDB
5XDG
Q9LBX2 200.3 Da LogP 2.83 TPSA 17.1 ✓ Ro5 ✓ Clean c1ccc2c(c1)-c3ccccc3S2=O
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…
IND RCSB PDB
5XDC
Q9LBX2 117.2 Da LogP 2.17 TPSA 15.8 ✓ Ro5 ✓ Clean c1ccc2c(c1)cc[nH]2

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.