KpKP13 Protein target profile

Homoserine kinase

Accession: KP13_01992

Gene: thrB AHE46430.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GMA8
Length 309
Pocket druggability (P2Rank · AlphaFold DB model) 0.898
Direct ligand evidence 0 53 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
No hit
Gut microbiome similarity
3.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
97.22 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) 0.898
Structure A0A0H3GMA8
Pocket Pocket 1
Druggability (FPocket) 0.651
Structure A0A0H3GMA8
Pocket Pocket 1
ColabFold model
P2Rank 0.923 · Pocket 1
FPocket 0.815 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 153 / 4744 genomes with a hit
Prevalence 3.2%

Sequence

Primary amino-acid sequence viewer.

MVKVYAPASSANMSVGFDVLGAAVTPVDGTLLGDNVTVEAAEQFSLQNLGRFASKLPTAPQENIVYQCWESFCREIGKTVPVAMTLEKNMPIGSGLGSSACSVVAALVAMNEFCGKPLNETRMLALMGEMEGRISGSIHYDNVAPCYLGGMQLMIEENGIISQQVPGFDEWLWVLAYPGIKVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYTRQPQLAAKLMKDVIAEPYRTKLLPGFSEARQAAMEMGAQACGISGSGPTLFALCDKPDTAQRVADWLGAHYLQNQEGFVHICRLDTAGARVVG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0004413 Catalysis of the reaction: L-homoserine + ATP = O-phospho-L-homoserine + ADP + 2 H+.
  • GO:0006566 The chemical reactions and pathways involving threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0009088 The chemical reactions and pathways resulting in the formation of L-threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
167 298 FunFam G3DSA:3.30.70.890:FF:000002 Homoserine kinase
1 166 FunFam G3DSA:3.30.230.10:FF:000020 Homoserine kinase
2 308 Hamap MF_00384 Homoserine kinase [thrB].
2 308 InterPro IPR000870 Homoserine kinase
2 308 NCBIfam TIGR00191 homoserine kinase
211 284 Pfam PF08544 GHMP kinases C terminal
211 284 InterPro IPR013750 GHMP kinase, C-terminal domain
1 309 PIRSF PIRSF000676 Homoser_kin
1 309 InterPro IPR000870 Homoserine kinase
167 298 Gene3D G3DSA:3.30.70.890 -
167 298 InterPro IPR036554 GHMP kinase, C-terminal domain superfamily
175 192 PRINTS PR00958 Homoserine kinase signature
254 269 PRINTS PR00958 Homoserine kinase signature
137 150 PRINTS PR00958 Homoserine kinase signature
9 24 PRINTS PR00958 Homoserine kinase signature
97 112 PRINTS PR00958 Homoserine kinase signature
1 166 Gene3D G3DSA:3.30.230.10 -
1 166 InterPro IPR014721 Ribosomal protein S5 domain 2-type fold, subgroup
2 308 PANTHER PTHR20861 HOMOSERINE/4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE
90 101 ProSitePatterns PS00627 GHMP kinases putative ATP-binding domain.
90 101 InterPro IPR006203 GHMP kinase, ATP-binding, conserved site
85 150 Pfam PF00288 GHMP kinases N terminal domain
85 150 InterPro IPR006204 GHMP kinase N-terminal domain
172 289 SUPERFAMILY SSF55060 GHMP Kinase, C-terminal domain
172 289 InterPro IPR036554 GHMP kinase, C-terminal domain superfamily
1 160 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like
1 160 InterPro IPR020568 Ribosomal protein S5 domain 2-type fold

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
0.898
Likely same site as FPocket 1 2.4 Å 20 shared residues 83% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.048
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.013
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
0.651 Unusual size
Likely same site as P2Rank 1 2.4 Å 20 shared residues 83% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:91-101
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_A0A0H3GMA8
AlphaFold DB full sequence Viewing
ColabFold KP13_01992
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.

53 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 3 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
AGS PDB via homolog 523.2 Da · LogP -1.51 · TPSA 262.1 Open detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
CDM PDB via homolog Detail RCSB PDB
ZINC12501520 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC3874716 ZINC proposed compound · Tanimoto 1.000 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
AGS RCSB PDB Q58504 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 P9WKG7 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)…
CDM RCSB PDB P9WKG7 521.3 Da LogP -3.20 TPSA 273.6 3 viol. ✓ Clean C[C@](CO)([C@@H](CO[P@](=O)(O)O[P@](=O)(O)OC[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.

Cross-references

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