Protein profile

PA0593

4-hydroxythreonine-4-phosphate dehydrogenase

Genome: NC_002516.2

Gene: PA0593 pdxA Structure source: Experimental + AlphaFold UniProt Q9I5U4

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Amino acids 328

Annotations 9

Features 10

PDB binders 2

Druggability 0.279

Overview

Basic information about this protein and its source genome.

Accession: PA0593
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA0593 pdxA
Status: annotated
Amino acids: 328
Structure source: Experimental + AlphaFold

1.1.1.262

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0050570 Catalysis of the reaction: 4-(phosphooxy)-L-threonine + NAD+ = 3-amino-2-oxopropyl phosphate + CO2 + NADH. GO:0050897 Binding to a cobalt ion (Co2+). GO:0000287 Binding to a magnesium (Mg) ion. GO:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH. GO:0008270 Binding to a zinc ion (Zn).

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 0.279

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1.1.1.262

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0050570 Catalysis of the reaction: 4-(phosphooxy)-L-threonine + NAD+ = 3-amino-2-oxopropyl phosphate + CO2 + NADH.
GO:0050897 Binding to a cobalt ion (Co2+).
GO:0000287 Binding to a magnesium (Mg) ion.
GO:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
GO:0008270 Binding to a zinc ion (Zn).
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.

Sequence Features

Domain/signature hits from InterPro and related databases.

10 records

Show feature table

Start	End	DB	Term	Name
31	320	Pfam	PF04166	Pyridoxal phosphate biosynthetic protein PdxA
31	320	InterPro	IPR005255	PdxA family
2	327	Hamap	MF_00536	4-hydroxythreonine-4-phosphate dehydrogenase [pdxA].
2	327	InterPro	IPR037510	4-hydroxythreonine-4-phosphate dehydrogenase
5	324	NCBIfam	TIGR00557	4-hydroxythreonine-4-phosphate dehydrogenase PdxA
5	324	InterPro	IPR005255	PdxA family
1	328	Gene3D	G3DSA:3.40.718.10	Isopropylmalate Dehydrogenase
3	327	PANTHER	PTHR30004	4-HYDROXYTHREONINE-4-PHOSPHATE DEHYDROGENASE
3	327	InterPro	IPR005255	PdxA family
3	326	SUPERFAMILY	SSF53659	Isocitrate/Isopropylmalate dehydrogenase-like

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

1 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 1YXO	X-ray	2.01 Å	A,B	100.0% 1-328	PDBe RCSB PDBj File	Viewing
AlphaFold PA0593	AlphaFold	—	—	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
1				0.279
4				0.226

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	8.14	0.433
2	3.04	0.1
3	2.7	0.081
4	1.83	0.035

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
5				0.619
7				0.418

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
4TP	1PS6	P19624	215.1 Da LogP -2.13 TPSA 150.3	✓ Ro5	✓ Clean	`C([C@H]([C@@H](C(=O)O)N)O)OP(=O)(O)O`
POP	6E85	A0A1Y0PY16	176.0 Da LogP -2.08 TPSA 129.9	✓ Ro5	✓ Clean	`O[P@@](=O)([O-])O[P@@](=O)(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).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC12501558	0.594	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(…`
ZINC12501560	0.594	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O…`
ZINC12501562	0.594	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)…`
ZINC12501564	0.594	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(…`
ZINC1532623	0.594	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(…`
ZINC2047359	0.594	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)COP(=O…`
ZINC2545091	0.594	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O…`
ZINC3869602	0.594	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)COP(=…`
ZINC3869603	0.594	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)COP(=O…`
ZINC3869604	0.594	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC4887586	0.545	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887587	0.545	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887588	0.545	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887589	0.545	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC5975509	0.533	202.1 Da LogP -2.19 TPSA 127.5	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H](O)[C@H](O)CO`
ZINC100657408	0.529	259.2 Da LogP -3.30 TPSA 170.5	1 viol.	✓ Clean	`N[C@H](C=O)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC215934438	0.529	259.2 Da LogP -3.30 TPSA 170.5	1 viol.	✓ Clean	`N[C@H](C=O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC255961849	0.529	259.2 Da LogP -3.30 TPSA 170.5	1 viol.	✓ Clean	`N[C@H](C=O)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC255961850	0.529	259.2 Da LogP -3.30 TPSA 170.5	1 viol.	✓ Clean	`N[C@H](C=O)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC5132021	0.529	259.2 Da LogP -3.30 TPSA 170.5	1 viol.	✓ Clean	`N[C@@H](C=O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1529626	0.515	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC1532567	0.515	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1532851	0.515	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC30320708	0.515	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC3870277	0.515	310.1 Da LogP -2.50 TPSA 191.0	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1532601	0.500	200.1 Da LogP -1.98 TPSA 124.3	✓ Ro5	✓ Clean	`O=C[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC2516111	0.500	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)CO`
ZINC2522704	0.500	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC32786787	0.500	200.1 Da LogP -1.98 TPSA 124.3	✓ Ro5	✓ Clean	`O=C[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC3869233	0.500	266.0 Da LogP -1.34 TPSA 170.8	✓ Ro5	✓ Clean	`O=C(O)[C@H](COP(=O)(O)O)OP(=O)(O)O`
ZINC3869234	0.500	266.0 Da LogP -1.34 TPSA 170.8	✓ Ro5	✓ Clean	`O=C(O)[C@@H](COP(=O)(O)O)OP(=O)(O)O`
ZINC3869812	0.500	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC5830339	0.500	231.1 Da LogP -2.68 TPSA 156.5	1 viol.	✓ Clean	`O=C(NO)[C@H](O)[C@H](O)COP(=O)(O)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.