Target Pathogen

Overview

Basic information about this protein and its source genome.

Accession: PA0006
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA0006 gmhB
Status: annotated
Amino acids: 178
Structure source: AlphaFold

EC

3.1.3.82

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:0034200 Catalysis of the reaction: D-glycero-beta-D-manno-heptose 1,7-bisphosphate + H2O = D-glycero-beta-D-manno-heptose 1-phosphate + phosphate. GO:0000287 Binding to a magnesium (Mg) ion. GO:0008270 Binding to a zinc ion (Zn). GO:0097171 The chemical reactions and pathways resulting in the formation of ADP-L-glycero-beta-D-manno-heptose, an ADP-L-glycero-D-manno-heptose having beta-configuration at the anomeric centre of the heptose. ADP-L-glycero-beta-D-manno-heptose (also called ADP-L-beta-D-heptose or ADP-L-glycero-D-manno-heptose) is a nucleotide-sugar precursor of the inner core lipopolysaccharide (LPS) from D-glycero-beta-D-manno-heptose 7-phosphate. GO:0009103 The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Gut microbiome off-target: hit
Essential (DEG): Y
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 0.57

Structure –

Pocket –

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)

1

3.1.3.82

Gene Ontology (GO)

9

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0034200 Catalysis of the reaction: D-glycero-beta-D-manno-heptose 1,7-bisphosphate + H2O = D-glycero-beta-D-manno-heptose 1-phosphate + phosphate.
GO:0000287 Binding to a magnesium (Mg) ion.
GO:0008270 Binding to a zinc ion (Zn).
GO:0097171 The chemical reactions and pathways resulting in the formation of ADP-L-glycero-beta-D-manno-heptose, an ADP-L-glycero-D-manno-heptose having beta-configuration at the anomeric centre of the heptose. ADP-L-glycero-beta-D-manno-heptose (also called ADP-L-beta-D-heptose or ADP-L-glycero-D-manno-heptose) is a nucleotide-sugar precursor of the inner core lipopolysaccharide (LPS) from D-glycero-beta-D-manno-heptose 7-phosphate.
GO:0009103 The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
GO:0009244 The chemical reactions and pathways resulting in the formation of the core region of bacterial lipopolysaccharides, which contains ten saccharide residues.
GO:0016791 Catalysis of the hydrolysis of a phosphoric monoester, releasing a phosphate.
GO:0005975 The chemical reactions and pathways involving 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.

15 records

Show feature table

Start	End	DB	Term	Name
5	148	NCBIfam	TIGR01662	HAD-IIIA family hydrolase
5	148	InterPro	IPR006549	HAD-superfamily hydrolase,subfamily IIIA
4	178	Gene3D	G3DSA:3.40.50.1000	-
4	178	InterPro	IPR023214	HAD superfamily
101	170	Pfam	PF13242	HAD-hyrolase-like
6	146	CDD	cd07503	HAD_HisB-N
5	147	NCBIfam	TIGR01656	histidinol-phosphate phosphatase domain
5	147	InterPro	IPR006543	Histidinol-phosphate phosphatase
3	177	PANTHER	PTHR42891	D-GLYCERO-BETA-D-MANNO-HEPTOSE-1,7-BISPHOSPHATE 7-PHOSPHATASE
3	177	InterPro	IPR004446	D,D-heptose 1,7-bisphosphate phosphatase
3	178	FunFam	G3DSA:3.40.50.1000:FF:000168	D,D-heptose 1,7-bisphosphate phosphatase
1	174	PIRSF	PIRSF004682	GmhB
1	174	InterPro	IPR004446	D,D-heptose 1,7-bisphosphate phosphatase
2	177	SUPERFAMILY	SSF56784	HAD-like
2	177	InterPro	IPR036412	HAD-like 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

0 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA0006	AlphaFold	—	—	full sequence	—	Viewing

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				0.57

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.

21 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
GMB	3L8G	P63228	370.1 Da LogP -3.63 TPSA 223.7	1 viol.	✓ Clean	`C([C@@H]([C@@H]1[C@H]([C@@H]([C@@H]([C@@H](O1)O…`

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).

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
ZINC12502703	0.550	340.1 Da LogP -2.99 TPSA 203.4	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](OP(=O)(O)O)[C@H](O)[C@…`
ZINC4095589	0.550	340.1 Da LogP -2.99 TPSA 203.4	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](OP(=O)(O)O)[C@H](O)[C@@…`
ZINC13522068	0.525	310.1 Da LogP -2.35 TPSA 183.2	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](OP(=O)(O)O)[C@H](O)[C@@…`
ZINC3870205	0.525	310.1 Da LogP -2.35 TPSA 183.2	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](OP(=O)(O)O)[C@@H](O)[C…`
ZINC4095560	0.525	310.1 Da LogP -2.35 TPSA 183.2	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](OP(=O)(O)O)[C@H](O)[C@…`
ZINC1532536	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1O[C@@H](CO)[C@H](O)[C@@H](O)[C@…`
ZINC1532537	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1O[C@@H](CO)[C@H](O)[C@@H](O)[C…`
ZINC1532880	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1O[C@H](CO)[C@H](O)[C@@H](O)[C@…`
ZINC35976710	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1O[C@H](CO)[C@H](O)[C@@H](O)[C@@…`
ZINC3869662	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@@…`
ZINC3869663	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1O[C@@H](CO)[C@H](O)[C@H](O)[C@…`
ZINC3869664	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@…`
ZINC3869665	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1O[C@@H](CO)[C@@H](O)[C@H](O)[C…`
ZINC3953999	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@…`
ZINC4073375	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H…`
ZINC4095569	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@…`
ZINC4095578	0.500	274.1 Da LogP -3.01 TPSA 174.0	1 viol.	✓ Clean	`O=C(O)[C@H]1O[C@H](OP(=O)(O)O)[C@H](O)[C@@H](O)…`
ZINC4096091	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H…`
ZINC4096092	0.500	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]…`
ZINC4096292	0.500	274.1 Da LogP -3.01 TPSA 174.0	1 viol.	✓ Clean	`O=C(O)[C@H]1O[C@H](OP(=O)(O)O)[C@H](O)[C@@H](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.

PA0006