KpKP13 Protein target profile

2-dehydro-3-deoxygluconokinase

Accession: KP13_00293

Gene: AHE42203.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GUG4
Length 309
Pocket druggability (P2Rank · AlphaFold DB model) 0.943
Direct ligand evidence 0 57 total records
Functional annotation 1 EC 7 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
2.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
42.765 Higher values support similarity to known essential genes.
DEG E-value
5.18e-82 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
96.7 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) 0.943
Structure A0A0H3GUG4
Pocket Pocket 1
Druggability (FPocket) 0.228
Structure A0A0H3GUG4
Pocket Pocket 19
ColabFold model
P2Rank 0.952 · Pocket 1
FPocket 0.125 · Pocket 7
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 104 / 4744 genomes with a hit
Prevalence 2.2%

Sequence

Primary amino-acid sequence viewer.

MSKKIAVIGECMIELSEKNGAVNRGFGGDTLNTSVYIARQTDASALSVHYVTALGTDAFSQQMLDSWQQENVNTDLIQRMADRLPGLYYIETDDTGERTFYYWRNEAAAKFWLESDRAAAICEELATFDYLYLSGISLAILSPVSRDKLFTLLRECRANGGKVIFDNNYRPRLWASQAETQQVYQEMLACTDIAFLTLDDEDALWGEKPVAEVIARTHAAGVEEVVVKRGADACLVSVSGQPLREVPAVRLAKEKVVDTTAAGDSFSAGYLAVRLTGGDAESAARRGHLTASTVIQYRGAIIPREAMPQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization
Unknown

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0008673 Catalysis of the reaction: 2-dehydro-3-deoxy-D-gluconate + ATP = 2-dehydro-3-deoxy-6-phospho-D-gluconate + ADP + 2 H+.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0019698 The chemical reactions and pathways resulting in the breakdown of D-galacturonate, the D-enantiomer of galacturonate, the anion of galacturonic acid.
  • GO:0042840 The chemical reactions and pathways resulting in the breakdown of D-glucuronate, the D-enantiomer of glucuronate.
  • GO:0006974 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

11 records
Show feature table
Start End DB Term Name
258 271 ProSitePatterns PS00584 pfkB family of carbohydrate kinases signature 2.
258 271 InterPro IPR002173 Carbohydrate/purine kinase, PfkB, conserved site
3 305 Pfam PF00294 pfkB family carbohydrate kinase
3 305 InterPro IPR011611 Carbohydrate kinase PfkB
4 301 CDD cd01166 KdgK
5 301 PANTHER PTHR43085 HEXOKINASE FAMILY MEMBER
1 309 Gene3D G3DSA:3.40.1190.20 -
1 309 InterPro IPR029056 Ribokinase-like
1 309 FunFam G3DSA:3.40.1190.20:FF:000011 2-dehydro-3-deoxygluconokinase, putative
2 302 SUPERFAMILY SSF53613 Ribokinase-like
2 302 InterPro IPR029056 Ribokinase-like

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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
0.943
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.046
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.035
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.024
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.005
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #19
0.228
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_A0A0H3GUG4
AlphaFold DB full sequence Viewing
ColabFold KP13_00293
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.

57 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ADN PDB via homolog 267.2 Da · LogP -1.98 · TPSA 139.5 Open detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
AP5 PDB via homolog Detail RCSB PDB
KDG PDB via homolog Detail RCSB PDB
KRM 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
ADN RCSB PDB Q584S0 267.2 Da LogP -1.98 TPSA 139.5 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP RCSB PDB O59128 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)…
AP5 RCSB PDB Q584S0 916.4 Da LogP -2.33 TPSA 480.5 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
KDG RCSB PDB Q53W83 178.1 Da LogP -2.26 TPSA 115.1 ✓ Ro5 ✓ Clean C([C@@H]([C@@H](CO)O)O)C(=O)C(=O)O
KRM RCSB PDB Q584S0 321.4 Da LogP 3.71 TPSA 50.4 ✓ Ro5 ✓ Clean c1ccc(cc1)Oc2ccc(cc2)c3cc(n[nH]3)N4CCOCC4
MLA RCSB PDB Q2YNY7 104.1 Da LogP -0.45 TPSA 74.6 ✓ Ro5 ✓ Clean C(C(=O)O)C(=O)O
RIB RCSB PDB A1A6H3 150.1 Da LogP -2.58 TPSA 90.2 ✓ Ro5 ✓ Clean C([C@@H]1[C@H]([C@H]([C@H](O1)O)O)O)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.