Protein profile

KP13_00816

Pyridoxine 5'-phosphate synthase

Genome: KpKP13

Gene: AHE43180.1 pdxJ Structure source: AlphaFold + ColabFold UniProt A0A0H3GTT4
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Amino acids 243
Annotations 5
Features 15
PDB binders 3
Druggability 0.216

Overview

Basic information about this protein and its source genome.

Accession
KP13_00816
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE43180.1 pdxJ
Status
annotated
Amino acids
243
Structure source
AlphaFold + ColabFold
EC
2.6.99.2
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. 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:0033856 Catalysis of the reaction: 1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = 2 H2O + H+ + phosphate + pyridoxine 5'-phosphate. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
94.239
DEG E-value
3.33e-169
Localization
Cytoplasmic
ColabFold pLDDT
97.29

Selected Druggability evidence

AlphaFold / UniProt model

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 0.216
Structure A0A0H3GTT4
Pocket Pocket 12
P2Rank 0.869
Structure A0A0H3GTT4
Pocket Pocket 1
ColabFold model
FPocket 0.408 · Pocket 13
P2Rank 0.871 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 271 / 4744 genomes with a hit
Normalized 0.057

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • 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:0033856 Catalysis of the reaction: 1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = 2 H2O + H+ + phosphate + pyridoxine 5'-phosphate.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
6 239 NCBIfam TIGR00559 pyridoxine 5'-phosphate synthase
6 239 InterPro IPR004569 Pyridoxal phosphate (active vitamin B6) biosynthesis PdxJ
1 243 Hamap MF_00279 Pyridoxine 5'-phosphate synthase [pdxJ].
1 243 InterPro IPR004569 Pyridoxal phosphate (active vitamin B6) biosynthesis PdxJ
4 242 PANTHER PTHR30456 PYRIDOXINE 5'-PHOSPHATE SYNTHASE
4 242 InterPro IPR004569 Pyridoxal phosphate (active vitamin B6) biosynthesis PdxJ
4 241 SUPERFAMILY SSF63892 Pyridoxine 5'-phosphate synthase
4 241 InterPro IPR036130 Pyridoxine 5'-phosphate synthase
5 238 CDD cd00003 PNPsynthase
5 238 InterPro IPR004569 Pyridoxal phosphate (active vitamin B6) biosynthesis PdxJ
1 243 FunFam G3DSA:3.20.20.70:FF:000042 Pyridoxine 5'-phosphate synthase
6 238 Pfam PF03740 Pyridoxal phosphate biosynthesis protein PdxJ
6 238 InterPro IPR004569 Pyridoxal phosphate (active vitamin B6) biosynthesis PdxJ
1 243 Gene3D G3DSA:3.20.20.70 Aldolase class I
1 243 InterPro IPR013785 Aldolase-type TIM barrel

3D Structure

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

3D visualization script Full viewer

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Structural evidence

0 + 2

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GTT4
AlphaFold — — full sequence — Viewing
ColabFold KP13_00816
ColabFold — — 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
12 0.216

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 14.87 0.737
2 1.71 0.03
3 1.06 0.007

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.

53 records

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
DXP
1IXN
P0A794 214.1 Da LogP -1.59 TPSA 124.3 ✓ Ro5 ✓ Clean CC(=O)[C@H]([C@@H](COP(=O)(O)O)O)O
G3P
1IXN
P0A794 172.1 Da LogP -1.55 TPSA 107.2 ✓ Ro5 ✓ Clean C([C@H](COP(=O)(O)O)O)O
PXP
1HO4
P0A794 249.2 Da LogP 0.20 TPSA 120.1 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CO)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.