Protein target profile

VK055_3869

3-deoxy-D-manno-octulosonate 8-phosphate phosphatase

Genome: KpATCC43816 Gene: yrbI AIK82419.1 3D evidence: Experimental + ColabFold model Metabolism 1 reaction UniProt A0A0H3GTS8
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Length 188
Pocket druggability 0.287
Metabolic reactions 1
Chokepoint Yes
Functional annotation 1 EC 5 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

Metabolic bottleneck Catalyzes a reaction that is the only producer or consumer of a metabolite in the imported metabolic model. Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. Central metabolic position More central than 94.7% of genes in this genome. No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. Review the complete evidence below

Risks to review

Human similarity Top human hit identity: 32.335%. Microbiome similarity 144 of 4744 screened genomes (3.0%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.29. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.02.

Evidence gaps

No ligand evidence No experimental PDB ligands, measured ChEMBL bioactivity, or proposed ZINC compound records are available.
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 (%)
32.335 Lower values reduce human off-target concern.
Human E-value
1.02e-18
Gut microbiome similarity
3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
57.062 Higher values support similarity to known essential genes.
DEG E-value
3.2000000000000004e-64 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.57 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.287
Structure 7T35
Pocket Pocket 5
P2Rank 0.021
Structure 7T35
Pocket Pocket 1
ColabFold model
FPocket 0.557 · Pocket 2
P2Rank 0.127 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 144 / 4744 genomes with a hit
Prevalence 3.0%

Cross-references

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

Sequence

UniProt A0A0H3GTS8

Structure

PDB 7T35

Pathways

KEGG R03350 BioCyc KDO-8PPHOSPHAT-RXN

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 Biosynthesis of various nucleotide sugars, no isoenzyme backup detected, more central than 94.7% of genes in this genome.

Relative network centrality 94.7% more central than 94.7% of genes in this genome
Chokepoint Chokepoint gene
Pathways
Biosynthesis of various nucleotide sugars
Catalyzed reaction

1 reaction 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.

MNNADAQLATCYGPVSQAFVDRAAKIRLLILDVDGVLSDGLIYMGNQGEELKAFNVRDGYGIRCALTSGIEVAIITGRKAKLVEDRCQTLGITHLYQGQSDKLLAFRDLTDKLHVRPEEVAYIGDDLIDWPVMAEVGLSVAVADAHPLLLPRANYVTRINGGRGAVREVCDLLLLAQGKLDEAKGQSI

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0016788 Catalysis of the hydrolysis of any ester bond.
  • GO:0019143 Catalysis of the reaction: 8-phospho-3-deoxy-D-manno-oct-2-ulosonate + H2O = 3-deoxy-D-manno-octulosonate + phosphate.
  • GO:0046872 Binding to a metal ion.
  • GO:0008781 Catalysis of the reaction: CTP + N-acylneuraminate = diphosphate + CMP-N-acylneuraminate.
  • GO:0009103 The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
13 188 PIRSF PIRSF006118 KDO8-P_Ptase
13 188 InterPro IPR010023 KdsC family
7 188 FunFam G3DSA:3.40.50.1000:FF:000029 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
21 181 SFLD SFLDG01138 C1.6.2: Deoxy-d-mannose-octulosonate 8-phosphate Phosphatase Like
21 181 InterPro IPR010023 KdsC family
26 171 CDD cd01630 HAD_KDO-like
27 142 NCBIfam TIGR01662 HAD-IIIA family hydrolase
27 142 InterPro IPR006549 HAD-superfamily hydrolase,subfamily IIIA
94 162 Pfam PF08282 haloacid dehalogenase-like hydrolase
24 180 PANTHER PTHR21485 HAD SUPERFAMILY MEMBERS CMAS AND KDSC
1 188 Gene3D G3DSA:3.40.50.1000 -
1 188 InterPro IPR023214 HAD superfamily
26 178 NCBIfam TIGR01670 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase, YrbI family
26 178 InterPro IPR010023 KdsC family
22 181 SUPERFAMILY SSF56784 HAD-like
22 181 InterPro IPR036412 HAD-like superfamily
21 181 SFLD SFLDS00003 Haloacid Dehalogenase

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 #5
0.287
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Surrounding area
Site 2 FPocket #1
0.265
Likely same site as P2Rank 2 2.4 Å 10 shared residues 100% of smaller site
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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.021
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Surrounding area
Site 2 P2Rank #2
0.011
Likely same site as FPocket 1 2.4 Å 10 shared residues 100% of smaller site
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Surrounding area
All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 1

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
PDB 7T35
X-ray 2.65 Å A
100.0% 1-188
PDBe RCSB PDBj File
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ColabFold VK055_3869
ColabFold — — full sequence — Loaded