Protein profile

PA0845

neutral ceramidase

Genome: NC_002516.2

Gene: PA0845 Structure source: Experimental + AlphaFold UniProt Q9I596

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Amino acids 670

Annotations 9

Features 15

PDB binders 2

Druggability 0.919

Overview

Basic information about this protein and its source genome.

Accession: PA0845
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA0845
Status: annotated
Amino acids: 670
Structure source: Experimental + AlphaFold

3.5.1.23

GO:0005576 The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0046872 Binding to a metal ion. GO:0017040 Catalysis of the reaction: an N-acylsphing-4-enine + H2O = a fatty acid + sphing-4-enine. GO:0046514 The chemical reactions and pathways resulting in the breakdown of ceramides, any N-acetylated sphingoid. GO:0042759 The chemical reactions and pathways resulting in the formation of a long-chain fatty acid. A long-chain fatty acid has an aliphatic tail containing 13 to 22 carbons.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 36.111
Human E-value: 3.16e-129
Gut microbiome off-target: hit
Essential (DEG): N
Localization: Unknown

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 0.919

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

3.5.1.23

Gene Ontology (GO)

GO:0005576 The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GO:0046872 Binding to a metal ion.
GO:0017040 Catalysis of the reaction: an N-acylsphing-4-enine + H2O = a fatty acid + sphing-4-enine.
GO:0046514 The chemical reactions and pathways resulting in the breakdown of ceramides, any N-acetylated sphingoid.
GO:0042759 The chemical reactions and pathways resulting in the formation of a long-chain fatty acid. A long-chain fatty acid has an aliphatic tail containing 13 to 22 carbons.
GO:0046512 The chemical reactions and pathways resulting in the formation of sphingosine (sphing-4-enine), trans-D-erytho-2-amino-octadec-4-ene-1,3-diol, a long chain amino diol sphingoid base that occurs in most sphingolipids in animal tissues.
GO:0051872 The chemical reactions and pathways resulting in the breakdown of sphingosine (sphing-4-enine), trans-D-erytho-2-amino-octadec-4-ene-1,3-diol, a long chain amino diol sphingoid base that occurs in most sphingolipids in animal tissues.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records

Show feature table

Start	End	DB	Term	Name
17	24	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	24	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
506	665	Pfam	PF17048	Neutral/alkaline non-lysosomal ceramidase, C-terminal
506	665	InterPro	IPR031331	Neutral/alkaline non-lysosomal ceramidase, C-terminal
25	670	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	24	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
5	16	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
1	4	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
282	665	PANTHER	PTHR12670	CERAMIDASE
282	665	InterPro	IPR006823	Neutral/alkaline nonlysosomal ceramidase
1	24	Phobius	SIGNAL_PEPTIDE	Signal peptide region
536	670	Gene3D	G3DSA:2.60.40.2300	-
536	670	InterPro	IPR038445	Neutral ceramidase, C-terminal domain superfamily
29	501	Pfam	PF04734	Neutral/alkaline non-lysosomal ceramidase, N-terminal
29	501	InterPro	IPR031329	Neutral/alkaline non-lysosomal ceramidase, N-terminal

3D Structure

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

Loading 3D structure...

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Structural evidence

2 + 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 2ZWS	X-ray	1.40 Å	A	96.4% 25-670	PDBe RCSB PDBj File	Viewing
PDB 2ZXC	X-ray	2.20 Å	A,B	96.4% 25-670	PDBe RCSB PDBj File	Loaded
AlphaFold PA0845	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
1				0.919
4				0.373
6				0.222

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	Score	Probability
1	33.61	0.947
2	5.55	0.265
3	4.53	0.194
4	3.47	0.126
5	2.98	0.097

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
4				0.789
14				0.616
2				0.275

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.

62 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.

Ligand	Source crystal	MW · LogP · TPSA	Lipinski	PAINS	SMILES
2ED	2ZXC 2.20 Å Open crystal	341.5 Da LogP 4.10 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC\C=C\[C@H]([C@@H](CO)NC(=O)C)O`
PLM	2ZWS 1.40 Å Open crystal	256.4 Da LogP 5.55 TPSA 37.3	1 viol.	✓ Clean	`CCCCCCCCCCCCCCCC(=O)O`

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.

No PDB ligands found through similar proteins.

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL4866400	Q9NR71	7.75	426.7 Da LogP 5.85 TPSA 81.6	1 viol.	✓ Clean	`CCCCCCCCCCCCC/C=C/[C@@H](O)[C@H](CO)NC(=O)NCCCC…`
CHEMBL4848172	Q9NR71	6.10	471.8 Da LogP 8.55 TPSA 49.3	1 viol.	✓ Clean	`CCCCCCCCCCCC/C=C/[C@@H](O)[C@@H](C)NC(=O)c1ccc(…`
CHEMBL2152033	Q9NR71	—	361.6 Da LogP 5.85 TPSA 49.3	1 viol.	✓ Clean	`CCCCCCCCCCCCCC(=O)NCC(O)c1ccc(C)cc1`
CHEMBL2152035	Q9NR71	—	348.5 Da LogP 4.93 TPSA 62.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)NCC(O)c1ccncc1`
CHEMBL2152042	Q9NR71	—	359.6 Da LogP 6.00 TPSA 46.2	1 viol.	✓ Clean	`CCCCCCCCCCCCCC(=O)NCC(=O)c1ccc(C)cc1`
CHEMBL2333182	Q9NR71	—	392.6 Da LogP 4.48 TPSA 95.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)N[C@H](CO)[C@H](O)c1ccc(N)cc1`
CHEMBL408217	Q9NR71	—	422.6 Da LogP 4.81 TPSA 112.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)N[C@H](CO)[C@H](O)c1ccc([N+](…`
CHEMBL4861323	Q9JHE3	—	491.7 Da LogP 6.42 TPSA 77.0	1 viol.	✓ Clean	`CCCCCCCCCCCC/C=C/[C@@H](O)[C@@H](C)NC(=O)c1ccc(…`
CHEMBL4865548	Q9NR71	—	395.7 Da LogP 7.08 TPSA 49.3	1 viol.	✓ Clean	`CCCCCCCCCCCC/C=C/[C@@H](O)[C@@H](C)NC(=O)CCCCCCC`
CHEMBL4878103	Q9JHE3	—	505.7 Da LogP 6.81 TPSA 77.0	2 viol.	✓ Clean	`CCCCCCCCCCCC/C=C/[C@@H](O)[C@@H](C)NC(=O)c1ccc(…`

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
ZINC137219384	1.000	327.5 Da LogP 3.71 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCC/C=C/[C@@H](O)[C@H](CO)NC(C)=O`
ZINC1529498	1.000	200.3 Da LogP 3.99 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)O`
ZINC1530417	1.000	228.4 Da LogP 4.77 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)O`
ZINC1628119	1.000	214.3 Da LogP 4.38 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)O`
ZINC202085159	1.000	285.4 Da LogP 2.54 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCC/C=C/[C@@H](O)[C@H](CO)NC(C)=O`
ZINC2053467455	1.000	341.5 Da LogP 4.10 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC=C[C@H](O)[C@H](CO)NC(C)=O`
ZINC2053467456	1.000	341.5 Da LogP 4.10 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC=C[C@H](O)[C@@H](CO)NC(C)=O`
ZINC2053467457	1.000	341.5 Da LogP 4.10 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC=C[C@@H](O)[C@H](CO)NC(C)=O`
ZINC2053467458	1.000	341.5 Da LogP 4.10 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC=C[C@@H](O)[C@@H](CO)NC(C)=O`
ZINC58590836	1.000	341.5 Da LogP 4.10 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC/C=C/[C@H](O)[C@@H](CO)NC(C)=O`
ZINC59676558	1.000	341.5 Da LogP 4.10 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC/C=C/[C@H](O)[C@H](CO)NC(C)=O`
ZINC85565725	1.000	341.5 Da LogP 4.10 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC/C=C\[C@H](O)[C@H](CO)NC(C)=O`
ZINC85605691	1.000	341.5 Da LogP 4.10 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC/C=C\[C@H](O)[C@@H](CO)NC(C)=O`
ZINC8830549	1.000	341.5 Da LogP 4.10 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC/C=C/[C@@H](O)[C@@H](CO)NC(C)=O`
ZINC8830550	1.000	341.5 Da LogP 4.10 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC/C=C/[C@@H](O)[C@H](CO)NC(C)=O`
ZINC138457918	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCC(=O)O`
ZINC138458029	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCC(=O)O`
ZINC144395054	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCC(=O)O`
ZINC14619628	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCCCC(=O)O`
ZINC196749828	0.850	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCC(=O)O`
ZINC2113934076	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCC(=O)O`
ZINC2113934082	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCC(=O)O`
ZINC2113934083	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCC(=O)O`
ZINC2243670	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCC(=O)O`
ZINC2569203	0.850	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCC(=O)O`
ZINC4798470	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCCC(=O)O`
ZINC5973005	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCC(=O)O`
ZINC71418182	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCC(=O)CCCCC(=O)O`
ZINC79244776	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCCC(=O)O`
ZINC86037082	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCCC(=O)O`
ZINC86037089	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCCCC(=O)O`
ZINC86039283	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCC(=O)O`
ZINC3160730	0.810	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCC(=O)O`
ZINC4582907	0.810	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCC(=O)O`
ZINC4727003	0.810	312.4 Da LogP 4.69 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCC(=O)CCCCCCCC(=O)O`
ZINC86037074	0.810	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)CCCC(=O)O`
ZINC2378801	0.800	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCC(=O)O`
ZINC97978494	0.789	355.6 Da LogP 4.49 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC/C=C/[C@@H](O)[C@H](CO)NC(=O)CC`
ZINC2113934081	0.762	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCCCCCC(=O)O`
ZINC2243668	0.762	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCC(=O)O`
ZINC2378799	0.762	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCC(=O)O`
ZINC33820423	0.762	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCCCC(=O)O`
ZINC3607770	0.756	268.3 Da LogP 0.52 TPSA 112.7	✓ Ro5	✓ Clean	`CCC(=O)N[C@H](CO)[C@H](O)c1ccc([N+](=O)[O-])cc1`
ZINC105429940	0.750	369.6 Da LogP 4.88 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC/C=C/[C@H](O)[C@@H](CO)NC(=O)CCC`
ZINC108380981	0.750	369.6 Da LogP 4.88 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC/C=C/[C@@H](O)[C@@H](CO)NC(=O)CCC`
ZINC2265369633	0.750	369.6 Da LogP 4.88 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC=C[C@@H](O)[C@H](CO)NC(=O)CCC`
ZINC2265369634	0.750	369.6 Da LogP 4.88 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC=C[C@@H](O)[C@@H](CO)NC(=O)CCC`
ZINC2265369635	0.750	369.6 Da LogP 4.88 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC=C[C@H](O)[C@@H](CO)NC(=O)CCC`
ZINC2265369636	0.750	369.6 Da LogP 4.88 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC=C[C@H](O)[C@H](CO)NC(=O)CCC`
ZINC97974172	0.750	369.6 Da LogP 4.88 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC/C=C/[C@H](O)[C@H](CO)NC(=O)CCC`

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.