Protein profile

PA3005

beta-hexosaminidase

Genome: NC_002516.2

Gene: PA3005 nagZ Structure source: Experimental + AlphaFold UniProt Q9HZK0

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Amino acids 332

Annotations 12

Features 12

PDB binders 10

Druggability 0.825

Overview

Basic information about this protein and its source genome.

Accession: PA3005
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA3005 nagZ
Status: annotated
Amino acids: 332
Structure source: Experimental + AlphaFold

3.2.1.52

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0016231 Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-glucosamine residues in N-acetyl-beta-D-glucosaminides. GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. GO:0051301 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. GO:0009252 The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.

Target profile

Computed evidence for target prioritization.

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

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 0.825

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)

3.2.1.52

Gene Ontology (GO)

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0016231 Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-glucosamine residues in N-acetyl-beta-D-glucosaminides.
GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
GO:0051301 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
GO:0009252 The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.
GO:0009254 The continual breakdown and regeneration of peptidoglycan required to maintain the bacterial cell wall. Peptidoglycans consist of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.
GO:0008360 Any process that modulates the surface configuration of a cell.
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:0004553 Catalysis of the hydrolysis of any O-glycosyl bond.
GO:0004563 Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records

Show feature table

Start	End	DB	Term	Name
4	289	PANTHER	PTHR30480	BETA-HEXOSAMINIDASE-RELATED
230	247	ProSitePatterns	PS00775	Glycosyl hydrolases family 3 active site.
230	247	InterPro	IPR019800	Glycoside hydrolase, family 3, active site
1	332	Gene3D	G3DSA:3.20.20.300	-
1	332	InterPro	IPR036962	Glycoside hydrolase, family 3, N-terminal domain superfamily
12	288	Pfam	PF00933	Glycosyl hydrolase family 3 N terminal domain
12	288	InterPro	IPR001764	Glycoside hydrolase, family 3, N-terminal
2	332	FunFam	G3DSA:3.20.20.300:FF:000001	Beta-hexosaminidase
4	330	Hamap	MF_00364	Beta-hexosaminidase [nagZ].
4	330	InterPro	IPR022956	Beta-hexosaminidase, bacterial
3	287	SUPERFAMILY	SSF51445	(Trans)glycosidases
3	287	InterPro	IPR017853	Glycoside hydrolase superfamily

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

7 + 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 5G1M	X-ray	1.80 Å	A,B	100.0% 1-332	PDBe RCSB PDBj File	Viewing
PDB 5G6T	X-ray	2.15 Å	A,B	100.0% 1-332	PDBe RCSB PDBj File	Loaded
PDB 5G3R	X-ray	2.18 Å	A,B	100.0% 1-332	PDBe RCSB PDBj File	Loaded
PDB 5G5U	X-ray	2.25 Å	A,B	100.0% 1-332	PDBe RCSB PDBj File	Loaded
PDB 5G2M	X-ray	3.00 Å	A,B	100.0% 1-332	PDBe RCSB PDBj File	Loaded
PDB 5G5K	X-ray	3.10 Å	A,B	100.0% 1-332	PDBe RCSB PDBj File	Loaded
PDB 5LY7	X-ray	3.10 Å	A,B	100.0% 1-332	PDBe RCSB PDBj File	Loaded
AlphaFold PA3005	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				0.825

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	16.08	0.769
2	8.86	0.474
3	3.81	0.147
4	2.06	0.046
5	1.98	0.042

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				0.327
1				0.267

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.

64 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
NOK	5G5K 3.10 Å Open crystal	204.2 Da LogP -2.82 TPSA 101.8	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1CN[C@@H]([C@H]([C@@H]1O)O)CO`

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
1BW	4HZM	Q8ZQ06	232.3 Da LogP -2.04 TPSA 101.8	✓ Ro5	✓ Clean	`CCCC(=O)N[C@H]1CN[C@@H]([C@H]([C@@H]1O)O)CO`
2CZ	4MSS	B4EA43	204.2 Da LogP -2.82 TPSA 101.8	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1CNC[C@@H]([C@H]([C@@H]1O)O)O`
8M7	5UTP	B4EA43	409.4 Da LogP 0.58 TPSA 149.7	✓ Ro5	✓ Clean	`CCC(CC)C(=O)N[C@@H]\1[C@H]([C@@H]([C@H](O/C1=N\…`
8MP	5UTR	B4EA43	232.3 Da LogP -2.04 TPSA 101.8	✓ Ro5	✓ Clean	`CCCC(=O)N[C@H]1CNC[C@@H]([C@H]([C@@H]1O)O)O`
C76	6JTK	Q5FA94	275.2 Da LogP -2.54 TPSA 119.3	✓ Ro5	✓ Clean	`C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)NC(=O)C…`
H9J	6DTE	A0A125HFC0	289.2 Da LogP -2.90 TPSA 130.2	1 viol.	✓ Clean	`C(C1[C@H]([C@@H](C([C@H]([C@@H]1O)O)NC(=O)C(F)(…`
NP6	3GS6	Q9KU37	381.4 Da LogP -0.05 TPSA 149.7	✓ Ro5	✓ Clean	`CCCC(=O)N[C@@H]\1[C@H]([C@@H]([C@H](O/C1=N\OC(=…`
OAN	5UTQ	B4EA43	353.3 Da LogP -0.83 TPSA 149.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]\1[C@H]([C@@H]([C@H](O/C1=N\OC(=O)…`
VPU	3GSM	Q9KU37	395.4 Da LogP 0.34 TPSA 149.7	✓ Ro5	✓ Clean	`CCCCC(=O)N[C@@H]\1[C@H]([C@@H]([C@H](O/C1=N\OC(…`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

Ligand	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL2047302	6.52	240.7 Da LogP -2.40 TPSA 101.8	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1CN[C@H](CO)[C@@H](O)[C@@H]1O.Cl`
CHEMBL2047303	—	312.8 Da LogP -1.90 TPSA 128.1	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1CN[C@H](CO)[C@@H](O)[C@@H]1O[C@H](…`
CHEMBL2047304	—	383.8 Da LogP -2.40 TPSA 157.2	1 viol.	✓ Clean	`CC(=O)N[C@H]1CN[C@H](CO)[C@@H](O)[C@@H]1O[C@H](…`
CHEMBL2047305	—	512.9 Da LogP -3.05 TPSA 223.6	2 viol.	✓ Clean	`CC(=O)N[C@H]1CN[C@H](CO)[C@@H](O)[C@@H]1O[C@H](…`

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
ZINC100071913	1.000	353.3 Da LogP -0.83 TPSA 149.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1/C(=N/OC(=O)Nc2ccccc2)O[C@H](CO)[…`
ZINC110339007	1.000	353.3 Da LogP -0.83 TPSA 149.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1/C(=N/OC(=O)Nc2ccccc2)O[C@H](CO)[…`
ZINC110343895	1.000	353.3 Da LogP -0.83 TPSA 149.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1/C(=N\OC(=O)Nc2ccccc2)O[C@H](CO)[…`
ZINC22046559	1.000	353.3 Da LogP -0.83 TPSA 149.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1/C(=N\OC(=O)Nc2ccccc2)O[C@H](CO)[…`
ZINC22046563	1.000	353.3 Da LogP -0.83 TPSA 149.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1/C(=N\OC(=O)Nc2ccccc2)O[C@H](CO)[…`
ZINC22046568	1.000	353.3 Da LogP -0.83 TPSA 149.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1/C(=N/OC(=O)Nc2ccccc2)O[C@@H](CO)…`
ZINC22046573	1.000	353.3 Da LogP -0.83 TPSA 149.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1/C(=N/OC(=O)Nc2ccccc2)O[C@@H](CO)…`
ZINC230164453	1.000	353.3 Da LogP -0.83 TPSA 149.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1/C(=N/OC(=O)Nc2ccccc2)O[C@H](CO)[…`
ZINC255993849	1.000	353.3 Da LogP -0.83 TPSA 149.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1C(=NOC(=O)Nc2ccccc2)O[C@H](CO)[C@…`
ZINC255993850	1.000	353.3 Da LogP -0.83 TPSA 149.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1C(=NOC(=O)Nc2ccccc2)O[C@H](CO)[C@…`
ZINC255993851	1.000	353.3 Da LogP -0.83 TPSA 149.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1C(=NOC(=O)Nc2ccccc2)O[C@H](CO)[C@…`
ZINC255993852	1.000	353.3 Da LogP -0.83 TPSA 149.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1C(=NOC(=O)Nc2ccccc2)O[C@H](CO)[C@…`
ZINC38599450	1.000	353.3 Da LogP -0.83 TPSA 149.7	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1/C(=N/OC(=O)Nc2ccccc2)O[C@H](CO)[C…`
ZINC44154746	1.000	353.3 Da LogP -0.83 TPSA 149.7	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1/C(=N/OC(=O)Nc2ccccc2)O[C@@H](CO)[…`
ZINC44154749	1.000	353.3 Da LogP -0.83 TPSA 149.7	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1/C(=N/OC(=O)Nc2ccccc2)O[C@H](CO)[C…`
ZINC575229162	1.000	353.3 Da LogP -0.83 TPSA 149.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1/C(=N\OC(=O)Nc2ccccc2)O[C@H](CO)[…`
ZINC77292968	1.000	353.3 Da LogP -0.83 TPSA 149.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1/C(=N/OC(=O)Nc2ccccc2)O[C@@H](CO)…`
ZINC77292971	1.000	353.3 Da LogP -0.83 TPSA 149.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1/C(=N/OC(=O)Nc2ccccc2)O[C@H](CO)[…`
ZINC5167384	0.967	204.2 Da LogP -2.82 TPSA 101.8	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1CN[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC299888362	0.740	312.3 Da LogP -0.98 TPSA 140.8	✓ Ro5	✓ Clean	`O=C(Nc1ccccc1)ON=C1O[C@H](CO)[C@@H](O)[C@H](O)[…`
ZINC514277674	0.722	352.3 Da LogP 0.26 TPSA 137.7	✓ Ro5	✓ Clean	`CC(=O)C[C@H]1/C(=N/OC(=O)Nc2ccccc2)O[C@H](CO)[C…`
ZINC1560405153	0.632	351.3 Da LogP 0.77 TPSA 149.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1C(O)=C(O)[C@@H](CO)O/C1=N\OC(=O)N…`
ZINC10128336	0.583	275.2 Da LogP -2.54 TPSA 119.3	✓ Ro5	✓ Clean	`O=C(N[C@H]1[C@H](O)[C@@H](O)[C@@H](CO)O[C@H]1O)…`
ZINC10128341	0.583	275.2 Da LogP -2.54 TPSA 119.3	✓ Ro5	✓ Clean	`O=C(N[C@H]1[C@H](O)[C@@H](O)[C@H](CO)O[C@H]1O)C…`
ZINC10128345	0.583	275.2 Da LogP -2.54 TPSA 119.3	✓ Ro5	✓ Clean	`O=C(N[C@H]1[C@H](O)[C@H](O)[C@@H](CO)O[C@H]1O)C…`
ZINC1727773	0.583	275.2 Da LogP -2.54 TPSA 119.3	✓ Ro5	✓ Clean	`O=C(N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O…`
ZINC2527939	0.583	275.2 Da LogP -2.54 TPSA 119.3	✓ Ro5	✓ Clean	`O=C(N[C@@H]1[C@@H](O)O[C@@H](CO)[C@H](O)[C@H]1O…`
ZINC4290140	0.583	275.2 Da LogP -2.54 TPSA 119.3	✓ Ro5	✓ Clean	`O=C(N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O)…`
ZINC5085902	0.583	275.2 Da LogP -2.54 TPSA 119.3	✓ Ro5	✓ Clean	`O=C(N[C@@H]1[C@H](O)O[C@H](CO)[C@H](O)[C@@H]1O)…`
ZINC5085903	0.583	275.2 Da LogP -2.54 TPSA 119.3	✓ Ro5	✓ Clean	`O=C(N[C@@H]1[C@H](O)O[C@@H](CO)[C@H](O)[C@@H]1O…`
ZINC5085904	0.583	275.2 Da LogP -2.54 TPSA 119.3	✓ Ro5	✓ Clean	`O=C(N[C@@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O…`
ZINC5085906	0.583	275.2 Da LogP -2.54 TPSA 119.3	✓ Ro5	✓ Clean	`O=C(N[C@@H]1[C@H](O)O[C@@H](CO)[C@@H](O)[C@@H]1…`
ZINC5439360	0.575	250.3 Da LogP -3.75 TPSA 145.3	1 viol.	✓ Clean	`C[C@H](N)C(=O)N[C@H]1[C@@H](O)O[C@@H](CO)[C@@H]…`
ZINC5439361	0.575	250.3 Da LogP -3.75 TPSA 145.3	1 viol.	✓ Clean	`C[C@@H](N)C(=O)N[C@H]1[C@@H](O)O[C@@H](CO)[C@@H…`
ZINC5439364	0.575	250.3 Da LogP -3.75 TPSA 145.3	1 viol.	✓ Clean	`C[C@H](N)C(=O)N[C@@H]1[C@@H](O)O[C@@H](CO)[C@@H…`
ZINC5439366	0.575	250.3 Da LogP -3.75 TPSA 145.3	1 viol.	✓ Clean	`C[C@@H](N)C(=O)N[C@@H]1[C@@H](O)O[C@@H](CO)[C@@…`
ZINC101135919	0.561	251.2 Da LogP -2.47 TPSA 128.5	✓ Ro5	✓ Clean	`CCOC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@H](O)[C@@H…`
ZINC257345629	0.561	251.2 Da LogP -2.47 TPSA 128.5	✓ Ro5	✓ Clean	`CCOC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@…`
ZINC257345630	0.561	251.2 Da LogP -2.47 TPSA 128.5	✓ Ro5	✓ Clean	`CCOC(=O)N[C@H]1[C@H](O)[C@H](O)[C@@H](CO)O[C@H]…`
ZINC39947801	0.561	251.2 Da LogP -2.47 TPSA 128.5	✓ Ro5	✓ Clean	`CCOC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H…`
ZINC43760879	0.561	251.2 Da LogP -2.47 TPSA 128.5	✓ Ro5	✓ Clean	`CCOC(=O)N[C@H]1[C@H](O)[C@@H](O)[C@@H](CO)O[C@H…`
ZINC102212099	0.548	262.2 Da LogP -2.79 TPSA 168.0	✓ Ro5	Alert	`[N-]=[N+]=NCC(=O)N[C@@H]1[C@@H](O)O[C@H](CO)[C@…`
ZINC102212101	0.548	262.2 Da LogP -2.79 TPSA 168.0	✓ Ro5	Alert	`[N-]=[N+]=NCC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@@…`
ZINC102212104	0.548	262.2 Da LogP -2.79 TPSA 168.0	✓ Ro5	Alert	`[N-]=[N+]=NCC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H…`
ZINC145874846	0.548	262.2 Da LogP -2.79 TPSA 168.0	✓ Ro5	Alert	`[N-]=[N+]=NCC(=O)N[C@@H]1[C@H](O)O[C@@H](CO)[C@…`
ZINC145875013	0.548	262.2 Da LogP -2.79 TPSA 168.0	✓ Ro5	Alert	`[N-]=[N+]=NCC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@H…`
ZINC145875367	0.548	262.2 Da LogP -2.79 TPSA 168.0	✓ Ro5	Alert	`[N-]=[N+]=NCC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@H]…`
ZINC200242680	0.548	262.2 Da LogP -2.79 TPSA 168.0	✓ Ro5	Alert	`[N-]=[N+]=NCC(=O)N[C@H]1[C@H](O)[C@@H](O)[C@@H]…`
ZINC97978457	0.548	262.2 Da LogP -2.79 TPSA 168.0	✓ Ro5	Alert	`[N-]=[N+]=NCC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@@…`
ZINC97978459	0.548	262.2 Da LogP -2.79 TPSA 168.0	✓ Ro5	Alert	`[N-]=[N+]=NCC(=O)N[C@H]1[C@H](O)[C@H](O)[C@@H](…`

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.