Target Pathogen

Overview

Basic information about this protein and its source genome.

Accession: PA1049
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: pdxH PA1049
Status: annotated
Amino acids: 215
Structure source: AlphaFold

EC

1.4.3.5

GO

GO:0010181 Binding to flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes. GO:0004733 Catalysis of the reaction: pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH4+ + H2O2. This activity can also oxidize pyridoxine 5'-phosphate to pyridoxal 5'-phosphate + H2O2. GO:0042823 The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6. GO:0008615 The chemical reactions and pathways resulting in the formation of pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds. GO:0016638 Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 50.0
Human E-value: 1.8700000000000002e-49
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 0.565

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MTQSLADMRREYTRDGLSEANAPSDPFSLFRQWFDDAVKTERLPVEPNAMTLATVDADGYPHCRILLLKGLDERGFTFFTNYESAKGRQLAANPRAAMTFFWPALERQVRIEGSVEKVTPEESDAYYQVRPLGSRLGAWASPQSRVIADRAELERLLADTERRFADQPPSCPEHWGGYRLLPQRIEFWQGRPSRLHDRLDYRRQDGGWLRERLAP

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

1.4.3.5

Gene Ontology (GO)

5

GO:0010181 Binding to flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
GO:0004733 Catalysis of the reaction: pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH4+ + H2O2. This activity can also oxidize pyridoxine 5'-phosphate to pyridoxal 5'-phosphate + H2O2.
GO:0042823 The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.
GO:0008615 The chemical reactions and pathways resulting in the formation of pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds.
GO:0016638 Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
14	215	FunFam	G3DSA:2.30.110.10:FF:000011	Chromosome 7, whole genome shotgun sequence
2	215	Gene3D	G3DSA:2.30.110.10	-
2	215	InterPro	IPR012349	FMN-binding split barrel
11	215	Hamap	MF_01629	Pyridoxine/pyridoxamine 5'-phosphate oxidase [pdxH].
11	215	InterPro	IPR000659	Pyridoxamine 5'-phosphate oxidase
175	215	Pfam	PF10590	Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region
175	215	InterPro	IPR019576	Pyridoxine 5'-phosphate oxidase, dimerisation, C-terminal
43	122	Pfam	PF01243	Pyridoxamine 5'-phosphate oxidase
43	122	InterPro	IPR011576	Pyridoxamine 5'-phosphate oxidase, putative
25	215	NCBIfam	TIGR00558	pyridoxamine 5'-phosphate oxidase
25	215	InterPro	IPR000659	Pyridoxamine 5'-phosphate oxidase
1	215	PIRSF	PIRSF000190	Pyd_amn-ph_oxd
1	215	InterPro	IPR000659	Pyridoxamine 5'-phosphate oxidase
8	215	SUPERFAMILY	SSF50475	FMN-binding split barrel
185	198	ProSitePatterns	PS01064	Pyridoxamine 5'-phosphate oxidase signature.
185	198	InterPro	IPR019740	Pyridoxamine 5'-phosphate oxidase, conserved site
5	215	PANTHER	PTHR10851	PYRIDOXINE-5-PHOSPHATE OXIDASE
5	215	InterPro	IPR000659	Pyridoxamine 5'-phosphate oxidase

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...

Legend High Medium Low

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 PA1049	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
1				0.565

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.

2 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
NNV	4HMT	Q51793	274.3 Da LogP 0.93 TPSA 99.0	✓ Ro5	✓ Clean	`C1C=CC2=NC3=C(C=CC[C@H]3C(=O)O)NC2[C@@H]1C(=O)O`
WUB	4HMX	Q396C5	228.3 Da LogP 2.21 TPSA 61.7	✓ Ro5	✓ Clean	`c1ccc2c(c1)N[C@H]3[C@@H](CC=CC3=N2)C(=O)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).

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.

PA1049