Protein profile

KP13_03548

Pyridoxine kinase

Genome: KpKP13

Gene: pdxK AHE43354.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GVX6
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Amino acids 288
Annotations 6
Features 12
PDB binders 8
Druggability 0.034

Overview

Basic information about this protein and its source genome.

Accession
KP13_03548
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
pdxK AHE43354.1
Status
annotated
Amino acids
288
Structure source
AlphaFold + ColabFold
EC
2.7.1.35
GO
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:0008902 Catalysis of the reaction: 4-amino-5-hydroxymethyl-2-methylpyrimidine + ATP = 4-amino-2-methyl-5-phosphomethylpyrimidine + ADP + 2 H+.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
29.461
Human E-value
5.8e-22
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
74.653
DEG E-value
9.89e-151
Localization
Cytoplasmic
ColabFold pLDDT
91.38

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 0.034
Structure A0A0H3GVX6
Pocket Pocket 8
P2Rank 0.968
Structure A0A0H3GVX6
Pocket Pocket 1
ColabFold model
FPocket 0.006 · Pocket 5
P2Rank 0.968 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 68 / 4744 genomes with a hit
Normalized 0.014

Sequence

Primary amino-acid sequence viewer.

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:0008902 Catalysis of the reaction: 4-amino-5-hydroxymethyl-2-methylpyrimidine + ATP = 4-amino-2-methyl-5-phosphomethylpyrimidine + ADP + 2 H+.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
22 273 CDD cd01173 pyridoxal_pyridoxamine_kinase
22 273 InterPro IPR004625 Pyridoxine kinase
18 274 PANTHER PTHR10534 PYRIDOXAL KINASE
18 274 InterPro IPR004625 Pyridoxine kinase
23 284 SUPERFAMILY SSF53613 Ribokinase-like
23 284 InterPro IPR029056 Ribokinase-like
94 269 Pfam PF08543 Phosphomethylpyrimidine kinase
94 269 InterPro IPR013749 Pyridoxamine kinase/Phosphomethylpyrimidine kinase
1 287 Gene3D G3DSA:3.40.1190.20 -
1 287 InterPro IPR029056 Ribokinase-like
22 279 NCBIfam TIGR00687 pyridoxal kinase
22 279 InterPro IPR004625 Pyridoxine kinase

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_A0A0H3GVX6
AlphaFold — — full sequence — Viewing
ColabFold KP13_03548
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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 31.25 0.938
2 1.66 0.028
3 1.47 0.02
4 0.87 0.003

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.

63 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
ANP
2AJP
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)…
GT0
6K92
A0A3S7X3C0 183.2 Da LogP 0.73 TPSA 62.6 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)CO)COC)O
GT1
4EN4
O00764 263.2 Da LogP 0.85 TPSA 109.1 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)COC)O
PE4
5ZW9
A0A0F7J8S0 354.4 Da LogP 0.11 TPSA 84.8 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCCOCCOCCO
PXL
3FHX
O00764 167.2 Da LogP 0.40 TPSA 70.4 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)CO)C=O)O
PXM
6K90
A0A3S7X3C0 168.2 Da LogP 0.05 TPSA 79.4 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)CO)CN)O
TEP
4EOH
O00764 180.2 Da LogP -1.04 TPSA 72.7 ✓ Ro5 ✓ Clean CN1c2c([nH]cn2)C(=O)N(C1=O)C
UEG
6K91
A0A3S7X3C0 169.2 Da LogP 0.08 TPSA 73.6 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)CO)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.