Protein target profile

KP13_00004

Ribokinase

Genome: KpKP13 Gene: AHE47115.1 rbsK 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GPH7
Length 310
Pocket druggability 0.713
Direct ligand evidence 0 56 total records
Functional annotation 0 EC 3 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 (%)
44.898 Lower values reduce human off-target concern.
Human E-value
3.14e-06
Gut microbiome similarity
2.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
82.848 Higher values support similarity to known essential genes.
DEG E-value
1.17e-179 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
95.42 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 0.713
Structure A0A0H3GPH7
Pocket Pocket 11
P2Rank 0.962
Structure A0A0H3GPH7
Pocket Pocket 1
ColabFold model
FPocket 0.2 · Pocket 19
P2Rank 0.957 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 130 / 4744 genomes with a hit
Prevalence 2.7%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MMKTAGKLVVLGSINADHILNLDAFPTPGETVTGHHYQVAFGGKGANQAVAAGRSGADIAFIACTGDDDIGERIRRQLASDKIDVAPVRAVAGEATGVALIFVNAEGENVIGIHAGANAALSVSQVEAEKERIASAQALLMQLESPLESVIAAAKIAHHHHTTVVLNPAPARELPDELLALVDIITPNETEAEKLTGIRVESDEDAAKAANVLHAKGIGTVMITLGSRGVWLSAEGESRRIPGFRVQAIDTIAAGDTFNGALVTALLEGTALPEAIRFAHAAAAIAVTRKGAQPSVPWRTEIDEFLAQQG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
  • GO:0006014 The chemical reactions and pathways involving D-ribose (ribo-pentose). As beta-D-ribofuranose, D-ribose forms the glycose group of all ribonucleosides, ribonucleotides and ribonucleic acids, and also of ribose phosphates, various glycosides, some coenzymes and some forms of vitamin B12.
  • GO:0004747 Catalysis of the reaction: ATP + D-ribose = ADP + D-ribose 5-phosphate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

31 records
Show feature table
Start End DB Term Name
7 298 CDD cd01174 ribokinase
7 298 InterPro IPR011877 Ribokinase
17 310 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
12 16 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
250 263 ProSitePatterns PS00584 pfkB family of carbohydrate kinases signature 2.
250 263 InterPro IPR002173 Carbohydrate/purine kinase, PfkB, conserved site
1 3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 16 Phobius SIGNAL_PEPTIDE Signal peptide region
4 11 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
3 309 FunFam G3DSA:3.40.1190.20:FF:000012 Ribokinase
7 308 SUPERFAMILY SSF53613 Ribokinase-like
7 308 InterPro IPR029056 Ribokinase-like
7 298 Pfam PF00294 pfkB family carbohydrate kinase
7 298 InterPro IPR011611 Carbohydrate kinase PfkB
6 304 Hamap MF_01987 Ribokinase [rbsK].
6 304 InterPro IPR011877 Ribokinase
1 309 Gene3D G3DSA:3.40.1190.20 -
1 309 InterPro IPR029056 Ribokinase-like
9 303 NCBIfam TIGR02152 ribokinase
9 303 InterPro IPR011877 Ribokinase
3 307 PANTHER PTHR10584 SUGAR KINASE
109 122 PRINTS PR00990 Ribokinase signature
109 122 InterPro IPR002139 Ribokinase/fructokinase
221 232 PRINTS PR00990 Ribokinase signature
221 232 InterPro IPR002139 Ribokinase/fructokinase
10 31 PRINTS PR00990 Ribokinase signature
10 31 InterPro IPR002139 Ribokinase/fructokinase
177 192 PRINTS PR00990 Ribokinase signature
177 192 InterPro IPR002139 Ribokinase/fructokinase
37 56 PRINTS PR00990 Ribokinase signature
37 56 InterPro IPR002139 Ribokinase/fructokinase

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 #11
0.713
Likely same site as P2Rank 1 6.5 Å 17 shared residues 85% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.962
Likely same site as FPocket 11 6.5 Å 17 shared residues 85% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.072
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.006
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:256-256 Proton acceptor
UniProt: Binding site:144-144
UniProt: Binding site:15-17
UniProt: Binding site:188-188
UniProt: Binding site:224-229
UniProt: Binding site:250-250
UniProt: Binding site:252-252
UniProt: Binding site:255-256
UniProt: Binding site:256-256
UniProt: Binding site:280-280
UniProt: Binding site:286-286
UniProt: Binding site:289-289
UniProt: Binding site:291-291
UniProt: Binding site:295-295
UniProt: Binding site:43-47
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_A0A0H3GPH7
AlphaFold DB full sequence Viewing
ColabFold KP13_00004
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.

56 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 6 records from similar proteins
Structural ligands 6 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
A12 PDB via homolog 425.2 Da · LogP -1.64 · TPSA 223.4 Open detail RCSB PDB
ACP PDB via homolog Detail RCSB PDB
AN2 PDB via homolog Detail RCSB PDB
KDG PDB via homolog Detail RCSB PDB
RAH 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
A12 RCSB PDB Q9H477 425.2 Da LogP -1.64 TPSA 223.4 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ACP RCSB PDB A0A3S7X0F5 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)…
AN2 RCSB PDB Q9H477 426.2 Da LogP -1.78 TPSA 238.4 2 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
RAH RCSB PDB P32143 324.2 Da LogP -3.21 TPSA 191.0 1 viol. ✓ Clean C([C@@H]1[C@H]([C@@H]([C@](O1)(COP(=O)(O)O)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.