KpATCC43816 Protein target profile

L-ribulokinase

Accession: VK055_2512

Gene: AIK81109.1 araB 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GJ58

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Length 569

Pocket druggability (P2Rank · AlphaFold DB model) 0.967

Metabolic reactions 2

Chokepoint Yes

Direct ligand evidence 0 27 total records

Functional annotation 1 EC 7 GO

Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Metabolic chokepoint Catalyzes a reaction that is the only producer or consumer of a metabolite in the imported metabolic model. Central metabolic position More central than 98.1% of genes in this genome. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.97. Review the complete evidence below

Risks to review

Evidence coverage

Core evidence streams are available for this target.

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 (%): 25.362 Lower values reduce human off-target concern.
Human E-value: 2.53e-20
Gut microbiome similarity: 3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 28.025 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT: 94.48 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) 0.967

Structure A0A0H3GJ58

Pocket Pocket 1

Druggability (FPocket) 0.818

Structure A0A0H3GJ58

Pocket Pocket 7

ColabFold model

P2Rank 0.964 · Pocket 1

FPocket 0.858 · Pocket 10

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 144 / 4744 genomes with a hit

Prevalence 3.0%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Attractive metabolic target: catalyzes a consuming chokepoint reaction in Pentose and glucuronate interconversions, no isoenzyme backup detected, more central than 98.1% of genes in this genome.

Relative network centrality 98.1% more central than 98.1% of genes in this genome

Chokepoint Chokepoint gene

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MAIAIGLDFGSDSVRALAVECASGAELATSVEWYPRWREGQYCDGANNRFRHHPRDYIESMEAALKSVLASLSAEQRADVVGIGVDSTGSTPAPVDAEGNVLALREEFADNPNAMFVLWKDHTAVEEAEAITRLCHQPGKEDYSRYIGGIYSSEWFWAKILHVTREDSAVAQAAASWVELCDWVPALLSGTTRPQDLRRGRCSAGHKSLWHESWGGLPPASFFDELDPIINQHLAWPLFTDTWTADVPVGTLSAEWAQRLGLPQSVAISGGAFDCHMGAVGAGAQPNALVKVIGTSTCDILIADKESVGERTVKGICGQVDGSVVPHFIGMEAGQSAFGDIYAWFGRILGWPLEQLAQQQPALREQIKASQKQLLPALTEAWANNPSLEHLPVVLDWFNGRRTPNANQRLKGVITDLNLATDAPALFGGLIAATAFGARAIMECFTEQGIPVNNVMALGGIARKNQVIMQACCDVLNRPLQIVASDQCCALGAAIFAAVAAGVYDDIPAAQQRMASQVETTLQPRPAQAQRFEQLYQRYQQWSVSAEQHYLPSAAKAEKAPQSQAALTH

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization: Cytoplasmic

Enzyme Commission (EC)

2.7.1.16

Gene Ontology (GO)

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0008741 Catalysis of the reaction: ATP + L(or D)-ribulose = ADP + L(or D)-ribulose 5-phosphate.
GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
GO:0019569 The chemical reactions and pathways resulting in the breakdown of L-arabinose into D-xylulose 5-phosphate.
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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0019150 Catalysis of the reaction: ATP + D-ribulose = ADP + D-ribulose 5-phosphate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records

Show feature table

Start	End	DB	Term	Name
2	514	CDD	cd07781	FGGY_RBK
2	514	InterPro	IPR005929	Ribulokinase
5	284	SUPERFAMILY	SSF53067	Actin-like ATPase domain
5	284	InterPro	IPR043129	ATPase, nucleotide binding domain
336	536	Gene3D	G3DSA:1.20.58.2240	-
353	373	Coils	Coil	Coil
2	550	NCBIfam	TIGR01234	ribulokinase
2	550	InterPro	IPR005929	Ribulokinase
5	526	Gene3D	G3DSA:3.30.420.40	-
1	558	Hamap	MF_00520	Ribulokinase [araB].
1	558	InterPro	IPR005929	Ribulokinase
291	501	Pfam	PF02782	FGGY family of carbohydrate kinases, C-terminal domain
291	501	InterPro	IPR018485	Carbohydrate kinase, FGGY, C-terminal
3	547	PANTHER	PTHR43435	RIBULOKINASE
285	542	SUPERFAMILY	SSF53067	Actin-like ATPase domain
285	542	InterPro	IPR043129	ATPase, nucleotide binding domain

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

0.967

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Surrounding area

Pocket 2 P2Rank #2

0.2

Likely same site as FPocket 7 2.6 Å 11 shared residues 100% of smaller site

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Surrounding area

Pocket 3 P2Rank #3

0.111

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Surrounding area

Pocket 4 P2Rank #4

0.052

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Surrounding area

Pocket 5 P2Rank #5

0.048

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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 #7

0.818 Unusual size

Likely same site as P2Rank 2 2.6 Å 11 shared residues 100% of smaller site

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Surrounding area

Pocket 2 FPocket #26

0.454 Unusual size

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Surrounding area

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.964

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Surrounding area

Pocket 2 P2Rank #2

0.135

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Surrounding area

Pocket 3 P2Rank #3

0.109

Likely same site as FPocket 10 2.2 Å 10 shared residues 100% of smaller site

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Surrounding area

Pocket 4 P2Rank #4

0.068

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Surrounding area

Pocket 5 P2Rank #5

0.026

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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_A0A0H3GJ58	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_2512	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.

27 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 24 similarity-based ZINC candidates

Best available ligand signal

BTB PDB via homolog 209.2 Da · LogP -3.01 · TPSA 104.4 Open detail RCSB PDB

QDK PDB via homolog Detail RCSB PDB

XUL PDB via homolog Detail RCSB PDB

ZINC1615342 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC100036265 ZINC proposed compound · Tanimoto 0.682 Detail ZINC

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
BTB RCSB PDB	3GG4	Q665C6	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`C(CO)N(CCO)C(CO)(CO)CO`
QDK RCSB PDB	3QDK	Q9KBQ3	150.1 Da LogP -2.74 TPSA 98.0	✓ Ro5	✓ Clean	`C([C@@H]([C@@H](C(=O)CO)O)O)O`
XUL RCSB PDB	3L0Q	Q665C6	150.1 Da LogP -2.74 TPSA 98.0	✓ Ro5	✓ Clean	`C([C@H]([C@@H](C(=O)CO)O)O)O`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC1615342 ZINC	1.000	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`OCCN(CCO)C(CO)(CO)CO`
ZINC100036265 ZINC	0.682	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC100071552 ZINC	0.682	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CO`
ZINC113074329 ZINC	0.682	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC13522679 ZINC	0.682	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)CO`
ZINC4353160 ZINC	0.682	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)CO`
ZINC8579422 ZINC	0.682	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC2334905 ZINC	0.522	261.4 Da LogP 1.10 TPSA 63.9	✓ Ro5	✓ Clean	`CC(C)CCN(CCC(C)C)C(CO)(CO)CO`
ZINC3159953 ZINC	0.522	261.4 Da LogP 1.38 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCN(CCCCC)C(CO)(CO)CO`
ZINC113364020 ZINC	0.500	330.5 Da LogP 3.75 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)[C@@H](O)[C@@H](O)CO`
ZINC113364022 ZINC	0.500	330.5 Da LogP 3.75 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)[C@H](O)[C@@H](O)CO`
ZINC113364024 ZINC	0.500	330.5 Da LogP 3.75 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)[C@@H](O)[C@H](O)CO`
ZINC113364025 ZINC	0.500	330.5 Da LogP 3.75 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)[C@H](O)[C@H](O)CO`
ZINC1529626 ZINC	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC1532567 ZINC	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1532851 ZINC	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC30320708 ZINC	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC31259596 ZINC	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)CO`
ZINC31259600 ZINC	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)CO`
ZINC3869804 ZINC	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)CO`
ZINC3869805 ZINC	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)CO`
ZINC5297554 ZINC	0.500	289.5 Da LogP 2.16 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCCN(CCCCCC)C(CO)(CO)CO`
ZINC97941822 ZINC	0.500	317.5 Da LogP 2.94 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCCCN(CCCCCCC)C(CO)(CO)CO`
ZINC97942927 ZINC	0.500	373.6 Da LogP 4.51 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCCCCCN(CCCCCCCCC)C(CO)(CO)CO`

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.

Sequence

UniProt A0A0H3GJ58

Pathways

KEGG R01526 BioCyc D-RIBULOKIN-RXN KEGG R02439 BioCyc RXN0-5116