KpATCC43816 Protein target profile

alpha-ribazole phosphatase

Accession: VK055_1862

Gene: cobC AIK80468.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 7 reactions UniProt A0A0H3GPW8
Length 209
Pocket druggability (P2Rank · AlphaFold DB model) 0.89
Metabolic reactions 7
Chokepoint Yes
Direct ligand evidence 0 55 total records
Functional annotation 1 EC 9 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.

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 (%)
29.762 Lower values reduce human off-target concern.
Human E-value
3.94e-11
Gut microbiome similarity
0.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
96.08 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) 0.89
Structure A0A0H3GPW8
Pocket Pocket 1
Druggability (FPocket) 0.52
Structure A0A0H3GPW8
Pocket Pocket 4
ColabFold model
P2Rank 0.905 · Pocket 1
FPocket 0.629 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 45 / 4744 genomes with a hit
Prevalence 0.9%

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 Porphyrin metabolism, no isoenzyme backup detected, more central than 90.1% of genes in this genome.

Relative network centrality 90.1% more central than 90.1% of genes in this genome
Chokepoint Chokepoint gene
Catalyzed reactions

7 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MKLWLVRHGETEANVAGLYSGHAPTPLTPRGVAQARALGERLRLAPFDKVFCSELARTGTTADLLLGDRAIPRERHPALNEMFFGDWEMRHHRDLQREDAENYAAWCADWQHAAPTNGESFQNFARRVSEFIPTLTDCRHLDHLLIVGHQGVLSLLTALLLQMPAAAMWHFPIAHSAWSLLEIRDDFTTLRVLNSQAVWQPQEEFPPDH

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0016868 Catalysis of the transfer of a phosphate group from one position to another within a single molecule.
  • GO:0009236 The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
  • GO:0043755 Catalysis of the reaction: alpha-ribazole 5'-phosphate + H2O = alpha-ribazole + phosphate.
  • GO:0006096 The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0004331 Catalysis of the reaction: D-fructose 2,6-bisphosphate + H2O = D-fructose-6-phosphate + phosphate.
  • GO:0045820 Any process that stops, prevents, or reduces the frequency, rate or extent of glycolysis.
  • GO:0043456 Any process that modulates the frequency, rate or extent of the pentose-phosphate shunt, the process in which glucose is oxidized, coupled to NADPH synthesis.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
1 199 SUPERFAMILY SSF53254 Phosphoglycerate mutase-like
1 199 InterPro IPR029033 Histidine phosphatase superfamily
2 183 PANTHER PTHR11931 PHOSPHOGLYCERATE MUTASE
2 183 InterPro IPR005952 Phosphoglycerate mutase 1
3 195 Pfam PF00300 Histidine phosphatase superfamily (branch 1)
3 195 InterPro IPR013078 Histidine phosphatase superfamily, clade-1
2 156 SMART SM00855 PGAM_5
2 156 InterPro IPR013078 Histidine phosphatase superfamily, clade-1
5 14 ProSitePatterns PS00175 Phosphoglycerate mutase family phosphohistidine signature.
5 14 InterPro IPR001345 Phosphoglycerate/bisphosphoglycerate mutase, active site
1 202 Gene3D G3DSA:3.40.50.1240 -
1 202 InterPro IPR029033 Histidine phosphatase superfamily
3 180 NCBIfam TIGR03162 alpha-ribazole phosphatase
3 180 InterPro IPR017578 Alpha-ribazole phosphatase, CobC
2 194 CDD cd07067 HP_PGM_like
2 194 InterPro IPR013078 Histidine phosphatase superfamily, clade-1

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
0.89
Likely same site as FPocket 4 3.5 Å 15 shared residues 94% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.027
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Surrounding area
Pocket 3 P2Rank #3
0.001
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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 #4
0.52
Likely same site as P2Rank 1 3.5 Å 15 shared residues 94% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:8-8 Tele-phosphohistidine intermediate
UniProt: Active site:81-81 Proton donor/acceptor
UniProt: Binding site:57-57
UniProt: Binding site:7-14
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_A0A0H3GPW8
AlphaFold DB full sequence Viewing
ColabFold VK055_1862
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.

55 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
144 PDB via homolog 122.1 Da · LogP -1.72 · TPSA 60.7 Open detail RCSB PDB
3PG PDB via homolog Detail RCSB PDB
AGS PDB via homolog Detail RCSB PDB
G3H PDB via homolog Detail RCSB PDB
SEP 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
144 RCSB PDB N9V397 122.1 Da LogP -1.72 TPSA 60.7 ✓ Ro5 ✓ Clean C[N+](CO)(CO)CO
3PG RCSB PDB C4M5P9 186.1 Da LogP -1.46 TPSA 124.3 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)OP(=O)(O)O
AGS RCSB PDB P16118 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)…
G3H RCSB PDB P07953 170.1 Da LogP -1.34 TPSA 104.1 ✓ Ro5 ✓ Clean C([C@H](C=O)O)OP(=O)(O)O
SEP RCSB PDB D3DFG8 185.1 Da LogP -1.49 TPSA 130.1 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)N)OP(=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.