Protein target profile

KP13_05165

Pyridoxamine kinase

Genome: KpKP13 Gene: pdxY AHE44284.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GUH0
Length 286
Pocket druggability 0.7
Direct ligand evidence 0 68 total records
Functional annotation 1 EC 5 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

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
Hit
Human identity (%)
54.762 Lower values reduce human off-target concern.
Human E-value
8.2e-09
Gut microbiome similarity
2.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
50.694 Higher values support similarity to known essential genes.
DEG E-value
6.52e-99 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
97.48 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.7
Structure A0A0H3GUH0
Pocket Pocket 1
P2Rank 0.963
Structure A0A0H3GUH0
Pocket Pocket 1
ColabFold model
FPocket 0.687 · Pocket 3
P2Rank 0.963 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 121 / 4744 genomes with a hit
Prevalence 2.6%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

Primary amino-acid sequence viewer.

MKNILAIQSHVVFGHAGNSAAEFPMRRLGANVWPLNTVQFSNHTQYGKWTGCVMPPSHLTEIVQGIADIDKLQTCDAVLSGYLGSAEQGEHILGIVRQVKAANPAAKYFCDPVMGHPEKGCIVAPGVAEFHVRYALPASDIIAPNLVELEILCGHPVASVSEAVAAARELIAQGPEVVLVKHLARAGLSMDRFEMLLVTAEEAWHISRPLVDFGLRQPVGVGDVTSGLLLVKLLQGASLRDALEHVTAAVYEIMLATKNMQEYELQVVAAQDRIAVPEHCFSATRL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0009443 Any process that generates pyridoxal 5'-phosphate, the active form of vitamin B6, from derivatives of it without de novo synthesis.
  • GO:0008478 Catalysis of the reaction: ATP + pyridoxal = ADP + pyridoxal 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.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0000287 Binding to a magnesium (Mg) ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
2 279 PANTHER PTHR10534 PYRIDOXAL KINASE
2 279 InterPro IPR004625 Pyridoxine kinase
1 285 NCBIfam TIGR00687 pyridoxal kinase
1 285 InterPro IPR004625 Pyridoxine kinase
253 273 Coils Coil Coil
1 286 Gene3D G3DSA:3.40.1190.20 -
1 286 InterPro IPR029056 Ribokinase-like
1 278 SUPERFAMILY SSF53613 Ribokinase-like
1 278 InterPro IPR029056 Ribokinase-like
3 257 CDD cd01173 pyridoxal_pyridoxamine_kinase
3 257 InterPro IPR004625 Pyridoxine kinase
1 286 FunFam G3DSA:3.40.1190.20:FF:000008 Pyridoxal kinase PdxY
1 286 Hamap MF_01639 Pyridoxal kinase PdxY [pdxY].
1 286 InterPro IPR023685 Pyridoxal kinase PdxY
74 257 Pfam PF08543 Phosphomethylpyrimidine kinase
74 257 InterPro IPR013749 Pyridoxamine kinase/Phosphomethylpyrimidine kinase

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.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #1
0.7
Likely same site as P2Rank 2 7.1 Å 3 shared residues 30% of smaller site
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.963
Likely same site as FPocket 1 7.3 Å 13 shared residues 93% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.04
Likely same site as FPocket 1 7.1 Å 3 shared residues 30% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.015
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.003
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:111-111
UniProt: Binding site:143-143
UniProt: Binding site:148-148
UniProt: Binding site:181-181
UniProt: Binding site:208-211
UniProt: Binding site:223-223
UniProt: Binding site:44-45
UniProt: Binding site:9-9
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental 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_A0A0H3GUH0
AlphaFold DB full sequence Viewing
ColabFold KP13_05165
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.

68 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 18 records from similar proteins
Structural ligands 13 0 loaded crystals
Measured bioactivity 5 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ACP PDB via homolog 505.2 Da · LogP -1.52 · TPSA 269.9 Open detail RCSB PDB
AGS PDB via homolog Detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
D95 PDB via homolog Detail RCSB PDB
GT0 PDB via homolog Detail RCSB PDB

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
ACP RCSB PDB P82197 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AGS RCSB PDB Q8K183 523.2 Da LogP -1.51 TPSA 262.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP RCSB PDB O00764 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
D95 RCSB PDB Q8K183 384.4 Da LogP 2.60 TPSA 100.5 ✓ Ro5 ✓ Clean C[C@@H]1CC[C@H]2[C@H]([C@@H](O[C@H]3[C@@]24[C@H…
GT0 RCSB PDB O00764 183.2 Da LogP 0.73 TPSA 62.6 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)CO)COC)O
GT1 RCSB PDB O00764 263.2 Da LogP 0.85 TPSA 109.1 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)COC)O
NHE RCSB PDB Q141E8 207.3 Da LogP 0.80 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCS(=O)(=O)O
PXL RCSB PDB P77150 167.2 Da LogP 0.40 TPSA 70.4 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)CO)C=O)O
PXM RCSB PDB P82197 168.2 Da LogP 0.05 TPSA 79.4 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)CO)CN)O
R6C RCSB PDB P82197 355.4 Da LogP 3.17 TPSA 85.1 ✓ Ro5 ✓ Clean CC[C@H](CO)Nc1nc2c(c(n1)OCc3ccccc3)ncn2C(C)C
RMC RCSB PDB P82197 368.5 Da LogP 3.23 TPSA 79.1 ✓ Ro5 ✓ Clean CC[C@H](CO)Nc1nc2c(c(n1)[N@@](C)Cc3ccccc3)ncn2C…
RRC RCSB PDB P82197 354.5 Da LogP 3.20 TPSA 87.9 ✓ Ro5 ✓ Clean CC[C@H](CO)Nc1nc(c2c(n1)n(cn2)C(C)C)NCc3ccccc3
TEP RCSB PDB O00764 180.2 Da LogP -1.04 TPSA 72.7 ✓ Ro5 ✓ Clean CN1c2c([nH]cn2)C(=O)N(C1=O)C

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.