Strong target candidate with converging metabolic, structural and chemical evidence.
Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.
Main supporting evidence
Risks to review
Evidence coverage
Terms and data sources used on this page
PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.
AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.
ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.
pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.
FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.
Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.
PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.
ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.
ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.
LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.
Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.
DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.
Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.
EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.
KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.
Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.
Prioritization evidence
Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.
Off-target risk
- Human off-target
- No hit
- Gut microbiome similarity
- 5.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- Y
- DEG identity (%)
- 93.827 Higher values support similarity to known essential genes.
- DEG E-value
- 8.83e-169 Smaller values mean stronger essential-gene similarity.
Structure confidence
- ColabFold pLDDT
- 96.9 0-100 confidence; >70 supports local structural interpretation.
Binding-site evidence
AlphaFold DB / UniProt modelP2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.
Sequence
Primary amino-acid sequence viewer.
MAELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLHTRMNLEMAVTEEMLTIACETKPHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDACQRLADAGILVSLFIDADQAQIKAAADVGAPYIEIHTGCYADAKTDAEQARELERIAKAATYAASLGLKVNAGHGLTYHNVKAIAALPEMHELNIGHAIIGRAVMSGLKEAVAEMKRLMLEARG
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Subcellular localization
- Localization
- Cytoplasmic
Enzyme Commission (EC)
1Gene Ontology (GO)
4- 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: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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 6 | 238 | Pfam | PF03740 | Pyridoxal phosphate biosynthesis protein PdxJ |
| 6 | 238 | 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 |
| 1 | 243 | FunFam | G3DSA:3.20.20.70:FF:000042 | Pyridoxine 5'-phosphate synthase |
| 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 |
| 5 | 238 | CDD | cd00003 | PNPsynthase |
| 5 | 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 |
| 4 | 241 | SUPERFAMILY | SSF63892 | Pyridoxine 5'-phosphate synthase |
| 4 | 241 | InterPro | IPR036130 | Pyridoxine 5'-phosphate synthase |
3D structure
Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.
How colors and pocket overlays are used
Pocket details Inspect a specific pocket, or open the full viewer
- Method
- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
Selecting a pocket opens its details and centers the viewer without clearing other active layers. Use Focus this pocket when you want to hide the rest; use Surface for the wider residue environment.
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Residue sets
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Residue sets
All structural evidence
Structural evidence
0 + 2Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold DB
AF_A0A0H3GTT4
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_4612
|
ColabFold | — | — | full sequence | — | Loaded |
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.
Structural ligand evidence is available for this target.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, 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 |
|---|---|---|---|---|---|---|
| DXP RCSB PDB | 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 RCSB PDB | P0A794 | 172.1 Da LogP -1.55 TPSA 107.2 | ✓ Ro5 | ✓ Clean |
C([C@H](COP(=O)(O)O)O)O
|
|
| PXP RCSB PDB | P0A794 | 249.2 Da LogP 0.20 TPSA 120.1 | ✓ Ro5 | ✓ Clean |
Cc1c(c(c(cn1)COP(=O)(O)O)CO)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 |
|---|---|---|---|---|---|
| ZINC1532705 ZINC | 1.000 | 249.2 Da LogP 0.20 TPSA 120.1 | ✓ Ro5 | ✓ Clean |
Cc1ncc(COP(=O)(O)O)c(CO)c1O
|
| ZINC1532708 ZINC | 0.769 | 248.2 Da LogP 0.16 TPSA 125.9 | ✓ Ro5 | ✓ Clean |
Cc1ncc(COP(=O)(O)O)c(CN)c1O
|
| ZINC1529618 ZINC | 0.739 | 246.2 Da LogP -2.17 TPSA 136.7 | ✓ Ro5 | ✓ Clean |
O=P(O)(OC[C@@H](O)CO)OC[C@H](O)CO
|
| ZINC1529620 ZINC | 0.739 | 246.2 Da LogP -2.17 TPSA 136.7 | ✓ Ro5 | ✓ Clean |
O=P(O)(OC[C@@H](O)CO)OC[C@@H](O)CO
|
| ZINC1656021 ZINC | 0.711 | 233.2 Da LogP 1.01 TPSA 99.9 | ✓ Ro5 | ✓ Clean |
Cc1ncc(COP(=O)(O)O)c(C)c1O
|
| ZINC1532514 ZINC | 0.659 | 247.1 Da LogP 0.52 TPSA 117.0 | ✓ Ro5 | ✓ Clean |
Cc1ncc(COP(=O)(O)O)c(C=O)c1O
|
| ZINC5975509 ZINC | 0.640 | 202.1 Da LogP -2.19 TPSA 127.5 | ✓ Ro5 | ✓ Clean |
O=P(O)(O)OC[C@H](O)[C@H](O)CO
|
| ZINC1529626 ZINC | 0.633 | 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 ZINC | 0.633 | 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 ZINC | 0.633 | 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 ZINC | 0.633 | 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 ZINC | 0.633 | 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
|
| ZINC5830339 ZINC | 0.613 | 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
|
| ZINC2516111 ZINC | 0.593 | 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 ZINC | 0.593 | 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
|
| ZINC3869812 ZINC | 0.593 | 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
|
| ZINC1842949 ZINC | 0.578 | 243.2 Da LogP -0.49 TPSA 120.1 | ✓ Ro5 | ✓ Clean |
Cc1ncc(CO[C@@H](O)C(=O)O)c(CO)c1O
|
| ZINC639 ZINC | 0.578 | 243.2 Da LogP -0.49 TPSA 120.1 | ✓ Ro5 | ✓ Clean |
Cc1ncc(CO[C@H](O)C(=O)O)c(CO)c1O
|
| ZINC4095590 ZINC | 0.567 | 215.1 Da LogP -1.57 TPSA 122.2 | ✓ Ro5 | ✓ Clean |
NCCO[P@@](=O)(O)OC[C@H](O)CO
|
| ZINC4095591 ZINC | 0.567 | 215.1 Da LogP -1.57 TPSA 122.2 | ✓ Ro5 | ✓ Clean |
NCCO[P@@](=O)(O)OC[C@@H](O)CO
|
| ZINC12501558 ZINC | 0.563 | 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 ZINC | 0.563 | 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 ZINC | 0.563 | 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 ZINC | 0.563 | 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 ZINC | 0.563 | 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 ZINC | 0.563 | 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 ZINC | 0.563 | 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 ZINC | 0.563 | 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 ZINC | 0.563 | 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 ZINC | 0.563 | 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)…
|
| ZINC100065511 ZINC | 0.545 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C(CO)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O
|
| ZINC100085043 ZINC | 0.545 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C(CO)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O
|
| ZINC104869937 ZINC | 0.545 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C(CO)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O
|
| ZINC12502210 ZINC | 0.545 | 340.1 Da LogP -3.14 TPSA 211.3 | 1 viol. | ✓ Clean |
O=C(COP(=O)(O)O)[C@H](O)[C@H](O)[C@@H](O)COP(=O…
|
| ZINC12502212 ZINC | 0.545 | 340.1 Da LogP -3.14 TPSA 211.3 | 1 viol. | ✓ Clean |
O=C(COP(=O)(O)O)[C@H](O)[C@H](O)[C@H](O)COP(=O)…
|
| ZINC12502214 ZINC | 0.545 | 340.1 Da LogP -3.14 TPSA 211.3 | 1 viol. | ✓ Clean |
O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)[C@@H](O)COP(=…
|
| ZINC12502216 ZINC | 0.545 | 340.1 Da LogP -3.14 TPSA 211.3 | 1 viol. | ✓ Clean |
O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)[C@H](O)COP(=O…
|
| ZINC13537943 ZINC | 0.545 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C(CO)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O
|
| ZINC4523251 ZINC | 0.545 | 340.1 Da LogP -3.14 TPSA 211.3 | 1 viol. | ✓ Clean |
O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)[C@@H](O)COP(…
|
| ZINC4523255 ZINC | 0.545 | 340.1 Da LogP -3.14 TPSA 211.3 | 1 viol. | ✓ Clean |
O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)[C@H](O)COP(=…
|
| ZINC4523257 ZINC | 0.545 | 340.1 Da LogP -3.14 TPSA 211.3 | 1 viol. | ✓ Clean |
O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@@H](O)COP(=…
|
| ZINC4523259 ZINC | 0.545 | 340.1 Da LogP -3.14 TPSA 211.3 | 1 viol. | ✓ Clean |
O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@H](O)COP(=O…
|
| ZINC85994845 ZINC | 0.545 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C(CO)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O
|
| ZINC1680142 ZINC | 0.533 | 212.1 Da LogP -0.34 TPSA 96.2 | ✓ Ro5 | ✓ Clean |
C=CCOC[C@@H](O)COP(=O)(O)O
|
| ZINC5426687 ZINC | 0.533 | 212.1 Da LogP -0.34 TPSA 96.2 | ✓ Ro5 | ✓ Clean |
C=CCOC[C@H](O)COP(=O)(O)O
|
| ZINC100067589 ZINC | 0.531 | 334.2 Da LogP -4.34 TPSA 197.4 | 1 viol. | ✓ Clean |
O=[P@@](O)(OC[C@H](O)CO)O[C@H]1[C@H](O)[C@@H](O…
|
| ZINC100620818 ZINC | 0.531 | 334.2 Da LogP -4.34 TPSA 197.4 | 1 viol. | ✓ Clean |
O=[P@@](O)(OC[C@H](O)CO)O[C@H]1[C@@H](O)[C@@H](…
|
| ZINC2384698 ZINC | 0.531 | 244.2 Da LogP -0.14 TPSA 105.5 | ✓ Ro5 | ✓ Clean |
CCOC(OCC)[C@H](O)COP(=O)(O)O
|
| ZINC4521532 ZINC | 0.531 | 244.2 Da LogP -0.14 TPSA 105.5 | ✓ Ro5 | ✓ Clean |
CCOC(OCC)[C@@H](O)COP(=O)(O)O
|
| ZINC5132038 ZINC | 0.529 | 290.2 Da LogP -3.90 TPSA 185.0 | 1 viol. | ✓ Clean |
O=C(CO)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=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.
Cross-references
External database identifiers for this protein, its structures, ligands, and metabolic reactions.