Protein profile

KP13_02271

6-phospho-beta-glucosidase gmuD

Genome: KpKP13

Gene: AHE42843.1 gmuD Structure source: AlphaFold + ColabFold UniProt A0A0H3GX43

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Amino acids 470

Annotations 5

Features 17

PDB binders 7

Druggability 0.482

Overview

Basic information about this protein and its source genome.

Accession: KP13_02271
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE42843.1 gmuD
Status: annotated
Amino acids: 470
Structure source: AlphaFold + ColabFold

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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0008422 Catalysis of the hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose. GO:0016052 The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 29.87
Human E-value: 4.29e-11
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 97.4

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 0.482

Structure A0A0H3GX43

Pocket Pocket 9

P2Rank 0.896

Structure A0A0H3GX43

Pocket Pocket 1

ColabFold model

FPocket 0.394 · Pocket 22

P2Rank 0.893 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 57 / 4744 genomes with a hit

Normalized 0.012

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0008422 Catalysis of the hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose.
GO:0016052 The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records

Show feature table

Start	End	DB	Term	Name
5	459	PANTHER	PTHR10353	GLYCOSYL HYDROLASE
5	459	InterPro	IPR001360	Glycoside hydrolase family 1
2	455	SUPERFAMILY	SSF51445	(Trans)glycosidases
2	455	InterPro	IPR017853	Glycoside hydrolase superfamily
360	368	PRINTS	PR00131	Glycosyl hydrolase family 1 signature
360	368	InterPro	IPR001360	Glycoside hydrolase family 1
384	395	PRINTS	PR00131	Glycosyl hydrolase family 1 signature
384	395	InterPro	IPR001360	Glycoside hydrolase family 1
405	422	PRINTS	PR00131	Glycosyl hydrolase family 1 signature
405	422	InterPro	IPR001360	Glycoside hydrolase family 1
429	441	PRINTS	PR00131	Glycosyl hydrolase family 1 signature
429	441	InterPro	IPR001360	Glycoside hydrolase family 1
288	302	PRINTS	PR00131	Glycosyl hydrolase family 1 signature
288	302	InterPro	IPR001360	Glycoside hydrolase family 1
1	459	Gene3D	G3DSA:3.20.20.80	Glycosidases
2	458	Pfam	PF00232	Glycosyl hydrolase family 1
2	458	InterPro	IPR001360	Glycoside hydrolase family 1

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_A0A0H3GX43	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02271	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
3				0.291
1				0.017
17				0.01
2				0.001

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	29.42	0.896
2	4.87	0.179
3	3.01	0.079
4	2.56	0.059
5	2.29	0.047

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
22				0.394
26				0.284

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	20.23	0.852
2	5.13	0.236
3	3.44	0.124

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.

35 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
8P2	5N6T	Q08638	187.2 Da LogP -1.68 TPSA 101.4	✓ Ro5	✓ Clean	`C(C1C(C(C(C2C1O2)O)O)O)[N+]#N`
AM3	2WC3	Q08638	316.4 Da LogP -0.18 TPSA 105.8	✓ Ro5	✓ Clean	`CCCCCCCC/N=C\1/N2[C@H](CO1)[C@@H]([C@@H]([C@H](…`
GIM	7BZM	Q75I93	201.2 Da LogP -2.40 TPSA 100.6	✓ Ro5	✓ Clean	`c1c[n+]2c([nH]1)[C@@H]([C@H]([C@@H]([C@H]2CO)O)…`
IFM	1OIF	Q08638	147.2 Da LogP -2.08 TPSA 72.7	✓ Ro5	✓ Clean	`C1[C@@H]([C@H]([C@@H](CN1)O)O)CO`
JAZ	5FOO	Q99YP9	274.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`C(C1[C@H]([C@@H](C([C@H]([C@@H]1O)O)O)O)O)OP(=O…`
JJW	6QWI	P22073	348.4 Da LogP 0.05 TPSA 101.7	✓ Ro5	✓ Clean	`CCOCCOc1ccc(cc1)c2cn(nn2)C[C@H]3[C@@H]([C@@H](C…`
JSK	6R4K	P22073	391.4 Da LogP -0.43 TPSA 149.9	✓ Ro5	Alert	`[H]/N=N/NCCOCCOc1ccc(cc1)c2cn(nn2)C[C@H]3[C@@H]…`

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
CHEMBL402127	P12614	6.05	636.8 Da LogP 1.36 TPSA 168.7	1 viol.	✓ Clean	`COC(=O)CCCCCNC(=O)CCCCCN1[C@H](CO)[C@@H](O)[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
ZINC255989522	0.593	276.2 Da LogP -2.39 TPSA 147.7	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1S[C@H](O)[C@H](O)[C@H](O)[C@@…`
ZINC255989523	0.593	276.2 Da LogP -2.39 TPSA 147.7	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1S[C@H](O)[C@H](O)[C@H](O)[C@H…`
ZINC255989524	0.593	276.2 Da LogP -2.39 TPSA 147.7	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1S[C@H](O)[C@H](O)[C@@H](O)[C@…`
ZINC39044667	0.593	276.2 Da LogP -2.39 TPSA 147.7	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1S[C@@H](O)[C@H](O)[C@@H](O)[C@…`
ZINC44608494	0.593	276.2 Da LogP -2.39 TPSA 147.7	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1S[C@H](O)[C@H](O)[C@@H](O)[C@…`
ZINC95864639	0.593	276.2 Da LogP -2.39 TPSA 147.7	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1S[C@H](O)[C@H](O)[C@@H](O)[C@@…`
ZINC100351935	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@…`
ZINC1529564	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@@H](O)[C@H](O)[C@H](O)[C@…`
ZINC1532533	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@H](O)[C@@H](O)[C@H](O)[C@…`
ZINC1532857	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C…`
ZINC3581460	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C…`
ZINC38276879	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C@…`
ZINC38276880	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@@H](O)[C@H](O)[C@H…`
ZINC3869397	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C…`
ZINC3875374	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C@…`
ZINC3875375	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@…`
ZINC4095545	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C@…`
ZINC4095546	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@H…`
ZINC4096188	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@@H](O)[C@@H](O)[C@…`
ZINC8551507	0.533	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@H](O)[C@@H](O)[C@H](O)[C@…`
ZINC14982711	0.514	434.6 Da LogP 4.78 TPSA 86.7	✓ Ro5	✓ Clean	`CN(C)c1cccc2c(S(=O)(=O)NCCCCCCCCCCC(=O)O)cccc12`
ZINC2516261	0.514	364.5 Da LogP 2.83 TPSA 86.7	✓ Ro5	✓ Clean	`CN(C)c1cccc2c(S(=O)(=O)NCCCCCC(=O)O)cccc12`
ZINC12504154	0.500	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@@H](O)[C@@H]1O`
ZINC1532546	0.500	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@H](O)[C@@H](O)[C@H]1O`
ZINC4096190	0.500	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@H](O)[C@@H]1O`
ZINC4228241	0.500	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O`
ZINC4521831	0.500	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@@H](O)[C@@H]1O`

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.