Protein profile

KP13_31490

Beta-hexosaminidase

Genome: KpKP13

Gene: nagZ AHE45266.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GRI5

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Amino acids 340

Annotations 10

Features 12

PDB binders 7

Druggability 0.744

Overview

Basic information about this protein and its source genome.

Accession: KP13_31490
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: nagZ AHE45266.1
Status: annotated
Amino acids: 340
Structure source: AlphaFold + ColabFold

3.2.1.52

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: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. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. 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.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 95.86

Selected Druggability evidence

AlphaFold / UniProt model

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 0.744

Structure A0A0H3GRI5

Pocket Pocket 2

P2Rank 0.88

Structure A0A0H3GRI5

Pocket Pocket 1

ColabFold model

FPocket 0.355 · Pocket 4

P2Rank 0.893 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 141 / 4744 genomes with a hit

Normalized 0.03

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

3.2.1.52

Gene Ontology (GO)

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: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.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
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.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records

Show feature table

Start	End	DB	Term	Name
2	319	SUPERFAMILY	SSF51445	(Trans)glycosidases
2	319	InterPro	IPR017853	Glycoside hydrolase superfamily
1	337	FunFam	G3DSA:3.20.20.300:FF:000001	Beta-hexosaminidase
1	340	Gene3D	G3DSA:3.20.20.300	-
1	340	InterPro	IPR036962	Glycoside hydrolase, family 3, N-terminal domain superfamily
234	251	ProSitePatterns	PS00775	Glycosyl hydrolases family 3 active site.
234	251	InterPro	IPR019800	Glycoside hydrolase, family 3, active site
3	332	Hamap	MF_00364	Beta-hexosaminidase [nagZ].
3	332	InterPro	IPR022956	Beta-hexosaminidase, bacterial
9	300	Pfam	PF00933	Glycosyl hydrolase family 3 N terminal domain
9	300	InterPro	IPR001764	Glycoside hydrolase, family 3, N-terminal
3	319	PANTHER	PTHR30480	BETA-HEXOSAMINIDASE-RELATED

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

0 + 2

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GRI5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_31490	ColabFold	—	—	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
2				0.744
1				0.48

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	21.17	0.866
2	4.48	0.191
3	4.0	0.159
4	2.77	0.085

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				0.355

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	21.16	0.866
2	3.76	0.145
3	1.0	0.006

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.

61 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.

No PDB structure with a co-crystallized ligand found for this exact protein.

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`
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)(…`
NOK	5G5K	Q9HZK0	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`
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	2OXN	Q9KU37	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).

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
CHEMBL2047302	Q9HZK0	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	Q9HZK0	—	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	Q9HZK0	—	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	Q9HZK0	—	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](…`

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)[…`
ZINC10128336	1.000	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)…`
ZINC10128345	1.000	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…`
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)[…`
ZINC1727773	1.000	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…`
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)[…`
ZINC2527939	1.000	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…`
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…`
ZINC4290140	1.000	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)…`
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…`
ZINC5085902	1.000	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	1.000	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	1.000	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	1.000	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…`
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)[…`
ZINC263615178	0.722	263.3 Da LogP -2.05 TPSA 119.3	✓ Ro5	✓ Clean	`CC(C)(C)C(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O)…`
ZINC263615179	0.722	263.3 Da LogP -2.05 TPSA 119.3	✓ Ro5	✓ Clean	`CC(C)(C)C(=O)N[C@H]1[C@@H](O)O[C@H](CO)[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…`
ZINC409415373	0.686	222.2 Da LogP -3.55 TPSA 145.3	1 viol.	✓ Clean	`NC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@H](O)[C@@H]1O`
ZINC409415374	0.686	222.2 Da LogP -3.55 TPSA 145.3	1 viol.	✓ Clean	`NC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@H](O)[C@@H]1O`
ZINC225208891	0.649	236.2 Da LogP -3.28 TPSA 131.3	1 viol.	✓ Clean	`CNC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@H](O)[C@@H]…`
ZINC253389827	0.649	236.2 Da LogP -3.28 TPSA 131.3	1 viol.	✓ Clean	`CNC(=O)N[C@H]1[C@H](O)[C@H](O)[C@@H](CO)O[C@H]1O`
ZINC253389828	0.649	236.2 Da LogP -3.28 TPSA 131.3	1 viol.	✓ Clean	`CNC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H…`
ZINC253389829	0.649	236.2 Da LogP -3.28 TPSA 131.3	1 viol.	✓ Clean	`CNC(=O)N[C@H]1[C@H](O)[C@@H](O)[C@@H](CO)O[C@H]…`
ZINC25721491	0.649	236.2 Da LogP -3.28 TPSA 131.3	1 viol.	✓ Clean	`CNC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](O)[C@@H…`
ZINC25721497	0.649	236.2 Da LogP -3.28 TPSA 131.3	1 viol.	✓ Clean	`CNC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]…`
ZINC6792406	0.649	236.2 Da LogP -3.28 TPSA 131.3	1 viol.	✓ Clean	`CNC(=O)N[C@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[C@H…`
ZINC6792408	0.649	236.2 Da LogP -3.28 TPSA 131.3	1 viol.	✓ Clean	`CNC(=O)N[C@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[C@@…`
ZINC6792411	0.649	236.2 Da LogP -3.28 TPSA 131.3	1 viol.	✓ Clean	`CNC(=O)N[C@@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[C@…`
ZINC6792412	0.649	236.2 Da LogP -3.28 TPSA 131.3	1 viol.	✓ Clean	`CNC(=O)N[C@@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[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…`
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…`
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@@…`

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.