Genome KpKP13

Protein target profile

Rhamnulokinase

Accession: KP13_00591

Gene: rhaB AHE47066.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GGX5
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Length 488
Pocket druggability (P2Rank · AlphaFold DB model) 0.976
Direct ligand evidence 0 53 total records
Functional annotation 1 EC 8 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.

Main supporting evidence

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.98. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Microbiome similarity 76 of 4744 screened genomes (1.6%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.98) — check the ligand evidence before deprioritizing on off-target risk alone. Weak predicted binding pocket FPocket selected-pocket score 0.32.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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
1.6% 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
95.58 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) 0.976
Structure A0A0H3GGX5
Pocket Pocket 1
Druggability (FPocket) 0.316
Structure A0A0H3GGX5
Pocket Pocket 23
ColabFold model
P2Rank 0.971 · Pocket 1
FPocket 0.801 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 76 / 4744 genomes with a hit
Prevalence 1.6%

Cross-references

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

Sequence

UniProt A0A0H3GGX5

Sequence

Primary amino-acid sequence viewer.

MSIRHCVAVDLGASSGRVMLASYQPGPRALTLREIHRFTNSLQKVDGFDCWDVDSLEGEIRRGLEKVCEQGILIDSIGIDTWGVDYVLLDKQGQRVGLPISYRDDRTQGLLRHAEAQLGRAEIYRRSGIQFLPFNTLYQLRALVEQQPELVSQAAHALLIPDYFSFRLTGNLNWEYTNATTTQLVNINSDSWDETLLNWTGAPLAWFGKPTHPGNVIGHWICPQGNRIPVVAVASHDTASAVIASPLADRHAAYLSSGTWSLMGFESLTPYTCDAALQANITNEGGAEGRYRVLKNIMGLWLLQRVLKEQNVSDLQGLIARTAALPACRFIIDCNDDRFINPASMSAEIQAACRDAGQPVPESDAELARCIFDSLALLYARVLNELAALRGHPFSQLHIVGGGCQNTLLNQLCADACGIVVVAGPIEASTLGNIGIQLMTLDELANVDEFRQVVRGNAALTTFTPNPDSEIARFVAQFQPQQTKELCA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0019301 The chemical reactions and pathways resulting in the breakdown of rhamnose, the hexose 6-deoxy-L-mannose.
  • GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
  • GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
  • GO:0008993 Catalysis of the reaction: ATP + L-rhamnulose = ADP + L-rhamnulose 1-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:0004370 Catalysis of the reaction: ATP + glycerol = sn-glycerol 3-phosphate + ADP + 2 H+.
  • GO:0006071 The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
6 245 SUPERFAMILY SSF53067 Actin-like ATPase domain
6 245 InterPro IPR043129 ATPase, nucleotide binding domain
251 471 SUPERFAMILY SSF53067 Actin-like ATPase domain
251 471 InterPro IPR043129 ATPase, nucleotide binding domain
3 236 FunFam G3DSA:3.30.420.40:FF:000064 Rhamnulokinase
237 488 FunFam G3DSA:3.30.420.40:FF:000073 Rhamnulokinase
6 483 Hamap MF_01535 Rhamnulokinase [rhaB].
6 483 InterPro IPR013449 Rhamnulokinase
7 242 Pfam PF00370 FGGY family of carbohydrate kinases, N-terminal domain
7 242 InterPro IPR018484 Carbohydrate kinase, FGGY, N-terminal
5 437 CDD cd07771 FGGY_RhuK
5 437 InterPro IPR013449 Rhamnulokinase
1 236 Gene3D G3DSA:3.30.420.40 -
253 439 Pfam PF02782 FGGY family of carbohydrate kinases, C-terminal domain
253 439 InterPro IPR018485 Carbohydrate kinase, FGGY, C-terminal
7 470 PANTHER PTHR10196 SUGAR KINASE
7 459 NCBIfam TIGR02627 rhamnulokinase
7 459 InterPro IPR013449 Rhamnulokinase
237 488 Gene3D G3DSA:3.30.420.40 -

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
0.976
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Surrounding area
Pocket 2 P2Rank #2
0.206
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Surrounding area
Pocket 3 P2Rank #3
0.078
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Surrounding area
Pocket 4 P2Rank #4
0.049
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Surrounding area
Pocket 5 P2Rank #5
0.027
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #23
0.316
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:237-237 Proton acceptor
UniProt: Binding site:13-17
UniProt: Binding site:236-238
UniProt: Binding site:259-259
UniProt: Binding site:296-296
UniProt: Binding site:304-304
UniProt: Binding site:402-402
UniProt: Binding site:83-83
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_A0A0H3GGX5
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_00591
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
DXP PDB via homolog 214.1 Da · LogP -1.59 · TPSA 124.3 Open detail RCSB PDB
LFR PDB via homolog Detail RCSB PDB
XUL PDB via homolog Detail RCSB PDB
ZINC13551953 ZINC proposed compound · Tanimoto 0.875 Detail ZINC
ZINC13761953 ZINC proposed compound · Tanimoto 0.875 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
DXP RCSB PDB
3LL3
Q5FM28 214.1 Da LogP -1.59 TPSA 124.3 ✓ Ro5 ✓ Clean CC(=O)[C@H]([C@@H](COP(=O)(O)O)O)O
LFR RCSB PDB
2CGL
P32171 180.2 Da LogP -3.22 TPSA 110.4 ✓ Ro5 ✓ Clean C([C@H]1[C@@H]([C@H]([C@@](O1)(CO)O)O)O)O
XUL RCSB PDB
3LL3
Q5FM28 150.1 Da LogP -2.74 TPSA 98.0 ✓ Ro5 ✓ Clean C([C@H]([C@@H](C(=O)CO)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.