Target Pathogen

Overview

Basic information about this protein and its source genome.

Accession: PA5398
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: dgcA PA5398
Status: annotated
Amino acids: 686
Structure source: AlphaFold

GO

GO:0047865 Catalysis of the reaction: N,N-dimethylglycine + electron-transfer flavoprotein + H2O = sarcosine + formaldehyde + reduced electron-transfer flavoprotein. GO:0047866 Catalysis of the reaction: N,N-dimethylglycine + H2O + O2 = formaldehyde + H2O2 + sarcosine. GO:0010181 Binding to flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes. GO:0042426 The chemical reactions and pathways resulting in the breakdown of choline (2-hydroxyethyltrimethylammonium), an amino alcohol that occurs widely in living organisms as a constituent of certain types of phospholipids and in the neurotransmitter acetylcholine. GO:0031457 The chemical reactions and pathways resulting in the breakdown of glycine betaine, N-trimethylglycine. GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.

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 0.61

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6

GO:0047865 Catalysis of the reaction: N,N-dimethylglycine + electron-transfer flavoprotein + H2O = sarcosine + formaldehyde + reduced electron-transfer flavoprotein.
GO:0047866 Catalysis of the reaction: N,N-dimethylglycine + H2O + O2 = formaldehyde + H2O2 + sarcosine.
GO:0010181 Binding to flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
GO:0042426 The chemical reactions and pathways resulting in the breakdown of choline (2-hydroxyethyltrimethylammonium), an amino alcohol that occurs widely in living organisms as a constituent of certain types of phospholipids and in the neurotransmitter acetylcholine.
GO:0031457 The chemical reactions and pathways resulting in the breakdown of glycine betaine, N-trimethylglycine.
GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
392	414	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
609	623	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
660	667	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
6	352	CDD	cd04734	OYE_like_3_FMN
4	370	SUPERFAMILY	SSF51395	FMN-linked oxidoreductases
380	683	SUPERFAMILY	SSF51905	FAD/NAD(P)-binding domain
380	683	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
392	679	Gene3D	G3DSA:3.40.50.720	-
1	380	Gene3D	G3DSA:3.20.20.70	Aldolase class I
1	380	InterPro	IPR013785	Aldolase-type TIM barrel
608	624	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
393	412	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
487	616	Gene3D	G3DSA:3.50.50.60	-
487	616	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
392	643	Pfam	PF07992	Pyridine nucleotide-disulphide oxidoreductase
392	643	InterPro	IPR023753	FAD/NAD(P)-binding domain
1	647	PANTHER	PTHR43656	BINDING OXIDOREDUCTASE, PUTATIVE (AFU_ORTHOLOGUE AFUA_2G08260)-RELATED
1	380	FunFam	G3DSA:3.20.20.70:FF:000102	Putative N-methylproline demethylase
6	342	Pfam	PF00724	NADH:flavin oxidoreductase / NADH oxidase family
6	342	InterPro	IPR001155	NADH:flavin oxidoreductase/NADH oxidase, 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

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 PA5398	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				0.61

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.

3 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
FLC	6L6J	A0A0L8AFM7	189.1 Da LogP -5.25 TPSA 140.6	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O`
J5H	6QKR	E1YD54	921.7 Da LogP 1.13 TPSA 363.6	3 viol.	✓ Clean	`CC(C)(COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([…`
MDE	1PS9	P42593	994.9 Da LogP 0.91 TPSA 382.6	3 viol.	✓ Clean	`CCCCC[C@@H](C\C=C\C(=O)SCCNC(=O)CCNC(C(=O)C(C)(…`

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).

No virtual-screening candidates for this protein.

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.

PA5398