KpKP13 Protein target profile

Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase bifunctional protein

Accession: KP13_03172

Gene: AHE43612.1 thiD 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GSP3
Length 266
Pocket druggability (P2Rank · AlphaFold DB model) 0.959
Direct ligand evidence 0 54 total records
Functional annotation 1 EC 6 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
No hit
Gut microbiome similarity
4.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
56.538 Higher values support similarity to known essential genes.
DEG E-value
1.36e-89 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
94.06 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank'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.

Druggability (P2Rank) 0.959
Structure A0A0H3GSP3
Pocket Pocket 1
Druggability (FPocket) 0.388
Structure A0A0H3GSP3
Pocket Pocket 1
ColabFold model
P2Rank 0.959 · Pocket 1
FPocket 0.12 · Pocket 16
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 190 / 4744 genomes with a hit
Prevalence 4.0%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MKRINALTIAGTDPSGGAGIQADLKTFSALGAYGCSAITALVAQNTRGVQSVYRIEPDFVAAQLDSVFSDVRIDTTKIGMLAETDIVEAVAERLARYRVANVVLDTVMLAKSGDPLLSASAVETLRQRLLPQVSLITPNLPEAAALLDAPHARNEREMLEQGRALLALGCGAVLMKGGHLDDAESPDWLFTREGEQRFTAPRVQTKNTHGTGCTLSAALAALRPRHADWAATVIEAKAWLSAALAQADSLEVGHGIGPVHHFHAWW

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization
Unknown

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0009228 The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
  • GO:0008972 Catalysis of the reaction: ATP + 4-amino-2-methyl-5-phosphomethylpyrimidine = ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine.
  • 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+.
  • GO:0009229 The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
5 247 CDD cd01169 HMPP_kinase
5 247 InterPro IPR004399 Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase domain
5 265 SUPERFAMILY SSF53613 Ribokinase-like
5 265 InterPro IPR029056 Ribokinase-like
1 265 PANTHER PTHR20858 PHOSPHOMETHYLPYRIMIDINE KINASE
6 262 NCBIfam TIGR00097 bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase
6 262 InterPro IPR004399 Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase domain
13 260 Pfam PF08543 Phosphomethylpyrimidine kinase
13 260 InterPro IPR013749 Pyridoxamine kinase/Phosphomethylpyrimidine kinase
1 266 Gene3D G3DSA:3.40.1190.20 -
1 266 InterPro IPR029056 Ribokinase-like
1 266 FunFam G3DSA:3.40.1190.20:FF:000003 Phosphomethylpyrimidine kinase ThiD

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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.959
Likely same site as FPocket 1 7.0 Å 25 shared residues 83% of smaller site
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.102
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.388 Unusual size
Likely same site as P2Rank 1 7.0 Å 25 shared residues 83% of smaller site
Show in viewer
Surrounding area
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_A0A0H3GSP3
AlphaFold DB full sequence Viewing
ColabFold KP13_03172
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.

54 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 4 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 0 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
HMH PDB via homolog Detail RCSB PDB
PXL PDB via homolog Detail RCSB PDB
UEG PDB via homolog Detail RCSB PDB
ZINC105469665 ZINC proposed compound · Tanimoto 0.873 Detail ZINC

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 A0A0H3JTP0 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)…
HMH RCSB PDB P55882 139.2 Da LogP -0.14 TPSA 72.0 ✓ Ro5 ✓ Clean Cc1ncc(c(n1)N)CO
PXL RCSB PDB A0A0H3JTP0 167.2 Da LogP 0.40 TPSA 70.4 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)CO)C=O)O
UEG RCSB PDB A0A0H3JTP0 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.