Protein profile

PA1375

erythronate-4-phosphate dehydrogenase

Genome: NC_002516.2

Gene: PA1375 pdxB Structure source: Experimental + AlphaFold UniProt Q9I3W9
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Amino acids 380
Annotations 9
Features 21
PDB binders 7
Druggability 0.358

Overview

Basic information about this protein and its source genome.

Accession
PA1375
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA1375 pdxB
Status
annotated
Amino acids
380
Structure source
Experimental + AlphaFold
EC
1.1.1.290
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:0033711 Catalysis of the reaction: 4-phospho-D-erythronate + NAD+ = (R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + H+ + NADH. 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:0046983 The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits. GO:0036001 The chemical reactions and pathways resulting in the formation of pyridoxal 5'-phosphate, the active form of vitamin B6, from simpler components. 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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
34.058
Human E-value
1.55e-12
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 0.358
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

Gene Ontology (GO)

8
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0033711 Catalysis of the reaction: 4-phospho-D-erythronate + NAD+ = (R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + H+ + NADH.
  • 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:0046983 The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
  • GO:0036001 The chemical reactions and pathways resulting in the formation of pyridoxal 5'-phosphate, the active form of vitamin B6, from simpler components.
  • 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0016616 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
2 350 CDD cd12158 ErythrP_dh
2 350 InterPro IPR020921 Erythronate-4-phosphate dehydrogenase
33 277 Pfam PF00389 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
33 277 InterPro IPR006139 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
5 103 SUPERFAMILY SSF52283 Formate/glycerate dehydrogenase catalytic domain-like
197 213 ProSitePatterns PS00671 D-isomer specific 2-hydroxyacid dehydrogenases signature 3.
197 213 InterPro IPR029753 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site
92 257 FunFam G3DSA:3.40.50.720:FF:000093 Erythronate-4-phosphate dehydrogenase
107 256 Pfam PF02826 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
107 256 InterPro IPR006140 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain
1 363 Hamap MF_01825 Erythronate-4-phosphate dehydrogenase [pdxB].
1 363 InterPro IPR020921 Erythronate-4-phosphate dehydrogenase
1 277 Gene3D G3DSA:3.40.50.720 -
293 380 Gene3D G3DSA:3.30.1370.170 -
293 380 InterPro IPR038251 PdxB, dimerisation domain superfamily
33 274 PANTHER PTHR42938 FORMATE DEHYDROGENASE 1
289 376 Pfam PF11890 Domain of unknown function (DUF3410)
289 376 InterPro IPR024531 Erythronate-4-phosphate dehydrogenase, dimerisation domain
91 258 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
91 258 InterPro IPR036291 NAD(P)-binding domain superfamily
92 257 Gene3D G3DSA:3.40.50.720 -

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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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 2O4C
X-ray 2.30 Å A,B
100.0% 1-380
PDBe RCSB PDBj File
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AlphaFold PA1375
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
2 0.358

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 Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 16.64 0.783
2 1.98 0.042
3 1.17 0.01

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.

22 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.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
TLA
2O4C 2.30 Å Open crystal
150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=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.