Protein profile

PA2385

acyl-homoserine lactone acylase PvdQ

Genome: NC_002516.2

Gene: pvdQ PA2385 qsc112 Structure source: Experimental + AlphaFold UniProt Q9I194
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Amino acids 762
Annotations 12
Features 27
PDB binders 14
Druggability 0.951

Overview

Basic information about this protein and its source genome.

Accession
PA2385
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
pvdQ PA2385 qsc112
Status
annotated
Amino acids
762
Structure source
Experimental + AlphaFold
EC
3.5.1.97
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria). GO:0016811 Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide. GO:0042802 Binding to an identical protein or proteins. GO:0017000 The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms. GO:0071978 Bacterial-type flagellum-dependent cell motility in which the action of numerous flagella results in the smooth movement of a group of cells along a solid surface. Swarming motility is observed in groups of bacteria.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
Periplasmic

Selected Druggability evidence

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.951
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 11 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

11
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
  • GO:0016811 Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
  • GO:0042802 Binding to an identical protein or proteins.
  • GO:0017000 The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
  • GO:0071978 Bacterial-type flagellum-dependent cell motility in which the action of numerous flagella results in the smooth movement of a group of cells along a solid surface. Swarming motility is observed in groups of bacteria.
  • GO:0002049 The chemical reactions and pathways resulting in the formation of the siderochrome pyoverdine.
  • GO:0009372 The cell-cell signaling process in which single-celled organisms carry out coordinated responses by monitoring their own population density, and often also that of other microbes, by producing small, diffusible, signal molecules, detecting the concentration of these molecules, and triggering a signal transduction pathway when a certain threshold is reached. Quorum sensing can occur amongst microbial communities in the environment or within host organisms.
  • GO:0046677 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
  • GO:0044010 A process in which planktonically growing microorganisms of the same species grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.

Sequence Features

Domain/signature hits from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
5 760 PANTHER PTHR34218 PEPTIDASE S45 PENICILLIN AMIDASE
5 760 InterPro IPR002692 Penicillin/GL-7-ACA/AHL/aculeacin-A acylase
217 748 Gene3D G3DSA:3.60.20.10 Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
217 748 InterPro IPR029055 Nucleophile aminohydrolases, N-terminal
509 690 Gene3D G3DSA:1.10.1400.10 -
509 690 InterPro IPR043147 Penicillin amidase type, A-knob
24 193 FunFam G3DSA:1.10.439.10:FF:000003 Acyl-homoserine lactone acylase PvdQ
33 750 Pfam PF01804 Penicillin amidase
33 750 InterPro IPR002692 Penicillin/GL-7-ACA/AHL/aculeacin-A acylase
1 23 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
5 15 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
33 756 SUPERFAMILY SSF56235 N-terminal nucleophile aminohydrolases (Ntn hydrolases)
33 756 InterPro IPR029055 Nucleophile aminohydrolases, N-terminal
25 192 Gene3D G3DSA:1.10.439.10 Penicillin Amidohydrolase, domain 1
25 192 InterPro IPR023343 Penicillin amidase type, domain 1
1 23 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
1 23 Phobius SIGNAL_PEPTIDE Signal peptide region
292 366 Gene3D G3DSA:2.30.120.10 -
292 366 InterPro IPR043146 Penicillin amidase type, N-terminal domain, B-knob
35 744 CDD cd01936 Ntn_CA
179 759 PIRSF PIRSF001227 Pen_acylase
179 759 InterPro IPR014395 Penicillin/GL-7-ACA/AHL acylase
10 153 PIRSF PIRSF001227 Pen_acylase
10 153 InterPro IPR014395 Penicillin/GL-7-ACA/AHL acylase
1 4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
16 23 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
24 762 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

19 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 4WKS
X-ray 1.63 Å A
96.5% 28-762
PDBe RCSB PDBj File
Viewing
PDB 3L91
X-ray 1.66 Å A
97.0% 24-762
PDBe RCSB PDBj File
Loaded
PDB 4WKT
X-ray 1.78 Å A
96.5% 28-762
PDBe RCSB PDBj File
Loaded
PDB 2WYE
X-ray 1.80 Å A
97.0% 24-762
PDBe RCSB PDBj File
Loaded
PDB 4M1J
X-ray 1.80 Å A
96.5% 28-762
PDBe RCSB PDBj File
Loaded
PDB 3SRB
X-ray 1.80 Å A
96.3% 29-762
PDBe RCSB PDBj File
Loaded
PDB 5UBL
X-ray 1.80 Å A
71.7% 217-762
PDBe RCSB PDBj File
Loaded
PDB 2WYC
X-ray 1.90 Å A
97.0% 24-762
PDBe RCSB PDBj File
Loaded
PDB 2WYD
X-ray 1.90 Å A
97.0% 24-762
PDBe RCSB PDBj File
Loaded
PDB 4BTH
X-ray 1.90 Å A
97.0% 24-762
PDBe RCSB PDBj File
Loaded
PDB 3L94
X-ray 1.95 Å A
97.0% 24-762
PDBe RCSB PDBj File
Loaded
PDB 4K2F
X-ray 1.99 Å A
97.0% 24-762
PDBe RCSB PDBj File
Loaded
PDB 4WKU
X-ray 2.00 Å A
96.5% 28-762
PDBe RCSB PDBj File
Loaded
PDB 3SRC
X-ray 2.00 Å A
96.3% 29-762
PDBe RCSB PDBj File
Loaded
PDB 2WYB
X-ray 2.10 Å A
97.0% 24-762
PDBe RCSB PDBj File
Loaded
PDB 4WKV
X-ray 2.14 Å A
96.5% 28-762
PDBe RCSB PDBj File
Loaded
PDB 4K2G
X-ray 2.30 Å A
97.0% 24-762
PDBe RCSB PDBj File
Loaded
PDB 3SRA
X-ray 2.30 Å A
96.3% 29-762
PDBe RCSB PDBj File
Loaded
PDB 5UBK
X-ray 2.55 Å A
71.7% 217-762
PDBe RCSB PDBj File
Loaded
AlphaFold PA2385
AlphaFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
3 0.951
1 0.374

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 4.4 0.185
2 1.32 0.015
3 0.97 0.005

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.

82 records

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.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
28N
3SRC 2.00 Å Open crystal
269.1 Da LogP 1.48 TPSA 57.3 ✓ Ro5 ✓ Clean c1cc2c(cc1Br)N3C(=NOC3=O)CO2
28S
3SRB 1.80 Å Open crystal
264.1 Da LogP 2.99 TPSA 37.8 ✓ Ro5 ✓ Clean C=CCNc1c2cc(ccc2ncn1)Br
3LA
2WYC 1.90 Å Open crystal
214.3 Da LogP 3.17 TPSA 54.4 ✓ Ro5 ✓ Clean CCCCCCCCCC(=O)CC(=O)O
3QD
4WKS 1.63 Å Open crystal
73.9 Da LogP -0.52 TPSA 40.5 ✓ Ro5 ✓ Clean B(CC)(O)O
3QJ
4WKU 2.00 Å Open crystal
147.0 Da LogP 0.48 TPSA 60.7 ✓ Ro5 ✓ Clean [B-](CCCCCC)(O)(O)O
3QK
4WKV 2.14 Å Open crystal
175.1 Da LogP 1.26 TPSA 60.7 ✓ Ro5 ✓ Clean [B-](CCCCCCCC)(O)(O)O
83M
5UBK 2.55 Å Open crystal
658.8 Da LogP 2.83 TPSA 212.3 2 viol. ✓ Clean CCCCCCCCCCCCCC(=O)N[C@@H](CCC(=O)N[C@H](Cc1ccc(…
B0S
4M1J 1.80 Å Open crystal
228.2 Da LogP 3.77 TPSA 40.5 ✓ Ro5 ✓ Clean B(CCCCCCCCCCCCC)(O)O
BUB
4WKT 1.78 Å Open crystal
101.9 Da LogP 0.26 TPSA 40.5 ✓ Ro5 ✓ Clean B(CCCC)(O)O
DAO
2WYB 2.10 Å Open crystal
200.3 Da LogP 3.99 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCCCCCC(=O)O
MYR
3L94 1.95 Å Open crystal
228.4 Da LogP 4.77 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCCCCCCCC(=O)O
OCA
3L91 1.66 Å Open crystal
144.2 Da LogP 2.43 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCC(=O)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.