Protein target profile

PA3366

acylamide amidohydrolase

Genome: NC_002516.2

Gene: PA3366 amiE 3D evidence: Experimental + AlphaFold DB model UniProt P11436
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Length 346
Pocket druggability 0.71
Ligand records 57
EC / GO 1 / 5
Target summary

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

4 signals

Strengths

Strong predicted binding pocket FPocket selected-pocket score 0.71. This is a computational pocket signal, not binding validation. Structure available Experimental + AlphaFold DB model Ligand evidence via structure/bioactivity 6 structural and 1 bioactivity records.

Risks / watch

Human similarity Top human hit identity: 26.84%.

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
PA3366
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA3366 amiE
Status
annotated
Amino acids
346
3D evidence
Experimental + AlphaFold DB model
EC
3.5.1.4
GO
GO:0004040 Catalysis of the reaction: a monocarboxylic acid amide + H2O = a monocarboxylate + NH4+. GO:0016811 Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide. GO:0043605 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group. GO:0015976 A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary carbon sources and then activates genes to scavenge the last traces of the primary carbon source and to transport and metabolize alternative carbon sources such as carbon dioxide or carbonic acid. The utilization process begins when the cell or organism detects carbon levels, includes the activation of genes whose products detect, transport or metabolize carbon-containing substances, and ends when carbon is incorporated into the cell or organism's metabolism. GO:0006807 OBSOLETE. The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.

Target profile

Computed evidence for target prioritization.

Human off-target
Hit
Human identity (%)
26.84
Human E-value
5.94e-10
Gut microbiome off-target
Hit
Essential (DEG)
N
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 0.71
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MRHGDISSSNDTVGVAVVNYKMPRLHTAAEVLDNARKIAEMIVGMKQGLPGMDLVVFPEYSLQGIMYDPAEMMETAVAIPGEETEIFSRACRKANVWGVFSLTGERHEEHPRKAPYNTLVLIDNNGEIVQKYRKIIPWCPIEGWYPGGQTYVSEGPKGMKISLIICDDGNYPEIWRDCAMKGAELIVRCQGYMYPAKDQQVMMAKAMAWANNCYVAVANAAGFDGVYSYFGHSAIIGFDGRTLGECGEEEMGIQYAQLSLSQIRDARANDQSQNHLFKILHRGYSGLQASGDGDRGLAECPFEFYRTWVTDAEKARENVERLTRSTTGVAQCPVGRLPYEGLEKEA

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0004040 Catalysis of the reaction: a monocarboxylic acid amide + H2O = a monocarboxylate + NH4+.
  • GO:0016811 Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
  • GO:0043605 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
  • GO:0015976 A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary carbon sources and then activates genes to scavenge the last traces of the primary carbon source and to transport and metabolize alternative carbon sources such as carbon dioxide or carbonic acid. The utilization process begins when the cell or organism detects carbon levels, includes the activation of genes whose products detect, transport or metabolize carbon-containing substances, and ends when carbon is incorporated into the cell or organism's metabolism.
  • GO:0006807 OBSOLETE. The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
5 278 PANTHER PTHR43674 NITRILASE C965.09-RELATED
1 341 FunFam G3DSA:3.60.110.10:FF:000014 Aliphatic amidase
11 275 SUPERFAMILY SSF56317 Carbon-nitrogen hydrolase
11 275 InterPro IPR036526 Carbon-nitrogen hydrolase superfamily
13 260 ProSiteProfiles PS50263 Carbon-nitrogen hydrolase domain profile.
13 260 InterPro IPR003010 Carbon-nitrogen hydrolase
15 267 Pfam PF00795 Carbon-nitrogen hydrolase
15 267 InterPro IPR003010 Carbon-nitrogen hydrolase
1 341 Gene3D G3DSA:3.60.110.10 -
1 341 InterPro IPR036526 Carbon-nitrogen hydrolase superfamily
1 340 Hamap MF_01242 Aliphatic amidase [amiE].
1 340 InterPro IPR023719 Aliphatic amidase
13 310 CDD cd07565 aliphatic_amidase

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

1 + 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
PDB 2UXY
X-ray 1.25 Å A
98.6% 1-341
PDBe RCSB PDBj File
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AlphaFold DB PA3366
AlphaFold DB — — full sequence — Loaded
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
0.71
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Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.076
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Site 2 P2Rank #2
0.045
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Site 3 P2Rank #3
0.032
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Site 4 P2Rank #4
0.015
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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.

57 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 57 via homologs
Structural ligands 6 0 loaded crystals
Bioactive compounds 1 50 ZINC proposed compounds
Drug-like & clean 56 1 PAINS alerts
Best available ligand signal
ARF PDB via homolog 45.0 Da · LogP -0.90 · TPSA 43.1 Open detail RCSB PDB
Detail RCSB PDB ARF PDB via homolog
Detail RCSB PDB CDT PDB via homolog
Detail RCSB PDB CDV PDB via homolog
Detail RCSB PDB ING 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
ARF RCSB PDB
2E2L
O25836 45.0 Da LogP -0.90 TPSA 43.1 ✓ Ro5 ✓ Clean C(=O)N
CDT RCSB PDB
1UF5
P60327 192.2 Da LogP -0.14 TPSA 92.4 ✓ Ro5 ✓ Clean CSCC[C@H](C(=O)O)NC(=O)N
CDV RCSB PDB
1UF7
P60327 160.2 Da LogP -0.24 TPSA 92.4 ✓ Ro5 ✓ Clean CC(C)[C@H](C(=O)O)NC(=O)N
ING RCSB PDB
1UF8
P60327 208.2 Da LogP 0.35 TPSA 92.4 ✓ Ro5 ✓ Clean c1ccc(cc1)C[C@@H](C(=O)O)NC(=O)N
P4G RCSB PDB
5G3O
P59701 162.2 Da LogP 1.08 TPSA 27.7 ✓ Ro5 ✓ Clean CCOCCOCCOCC
ROP RCSB PDB
4GYL
Q9L543 73.1 Da LogP -0.12 TPSA 43.1 ✓ Ro5 ✓ Clean CCC(=O)N

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.