KpKP13 Protein target profile

2-(5''-triphosphoribosyl)-3'-dephosphocoenzyme-A synthase

Accession: KP13_01175

Gene: mdcB AHE44758.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GX15
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Length 280
Pocket druggability (P2Rank · AlphaFold DB model) 0.965
Functional annotation 1 EC 4 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

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.96, FPocket 0.83). Use the 3D pocket comparison to verify whether they identify the same site. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Strong predicted binding pocket FPocket selected-pocket score 0.83. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.96. Review the complete evidence below

Risks to review

Microbiome similarity 62 of 4744 screened genomes (1.3%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.96) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. 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
No hit
Gut microbiome similarity
1.3% 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
95.94 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) 0.965
Structure A0A0H3GX15
Pocket Pocket 1
Druggability (FPocket) 0.828
Structure A0A0H3GX15
Pocket Pocket 3
ColabFold model
P2Rank 0.95 · Pocket 1
FPocket 0.865 · Pocket 3
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 62 / 4744 genomes with a hit
Prevalence 1.3%

Cross-references

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

Sequence

UniProt A0A0H3GX15

Sequence

Primary amino-acid sequence viewer.

MKNLSPLHAESRVSWLAHTASACLIDEARLSPKPGLVDSRGNGAHQDLNLALMERSARSLQPTFHALAEQSWRRPADIALRETVGRLGREGEAQMMLATGGVNTHRGAIWALGLLVSAVAMLGGEGQSQAIADAAAALACLPDGFAPKSFSKGLRASRRWQVPGAREEAQCGFPHITRLALPQLQHSRARGASEPQAQLDALMAIMTSLSDTCVLSRAGMAGLQAMQQGACEVLAAGGCASFAGRAALARLDAIMLALNASPGGAADLLAATLFLDRVAG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization
Unknown

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0016310 The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
  • GO:0046917 Catalysis of the reaction: ATP + 3-dephospho-CoA = 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA + adenine.
  • GO:0051191 The chemical reactions and pathways resulting in the formation of a prosthetic group, the non-amino acid portion of certain protein molecules. Prosthetic groups may be inorganic or organic and are usually required for the biological activity of the protein.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

11 records
Show feature table
Start End DB Term Name
14 278 PANTHER PTHR30201 TRIPHOSPHORIBOSYL-DEPHOSPHO-COA SYNTHASE
14 278 InterPro IPR002736 Triphosphoribosyl-dephospho-CoA protein
1 23 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile.
1 280 Hamap MF_01883 2-(5''-triphosphoribosyl)-3'-dephosphocoenzyme-A synthase [mdcB].
1 280 InterPro IPR017555 Triphosphoribosyl-dephospho-CoA synthase
17 275 Pfam PF01874 ATP:dephospho-CoA triphosphoribosyl transferase
17 275 InterPro IPR002736 Triphosphoribosyl-dephospho-CoA protein
41 141 Gene3D G3DSA:1.10.4200.10 -
147 280 Gene3D G3DSA:1.10.4200.10 -
16 278 NCBIfam TIGR03132 triphosphoribosyl-dephospho-CoA synthase MdcB
16 278 InterPro IPR017555 Triphosphoribosyl-dephospho-CoA synthase

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
0.965
Likely same site as FPocket 3 7.9 Å 15 shared residues 75% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.459
Likely same site as FPocket 1 0.1 Å 16 shared residues 94% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.037
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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 #3
0.828
Likely same site as P2Rank 1 7.9 Å 15 shared residues 75% of smaller site
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Surrounding area
Pocket 2 FPocket #1
0.732
Likely same site as P2Rank 2 0.1 Å 16 shared residues 94% of smaller site
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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_A0A0H3GX15
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_01175
ColabFold — — full sequence — Loaded