KpKP13 Protein target profile

Gluconate 2-dehydrogenase cytochrome c subunit

Accession: KP13_05311

Gene: AHE44171.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GZ84
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Length 446
Pocket druggability (P2Rank · AlphaFold DB model) 0.998
Functional annotation 0 EC 6 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 1.00, FPocket 0.97). 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. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.97. This is a computational pocket signal, not binding validation. Review the complete evidence below

Risks to review

Microbiome similarity 45 of 4744 screened genomes (0.9%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 1.00) — check the ligand evidence before deprioritizing on off-target risk alone.

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
0.9% 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
88.4 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) 0.998
Structure A0A0H3GZ84
Pocket Pocket 1
Druggability (FPocket) 0.97
Structure A0A0H3GZ84
Pocket Pocket 23
ColabFold model
P2Rank 0.998 · Pocket 1
FPocket 0.995 · Pocket 28
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 45 / 4744 genomes with a hit
Prevalence 0.9%

Sequence

Primary amino-acid sequence viewer.

MMKMQWLSALVLGALSCAAFAEEAPADSNLIKQGEYLARAGDCVACHTNGKAGKPFAGGLPMETPIGTIYSTNITPDKEHGIGGYTFEEFDDAVRKGVRKDGSTLYPAMPYPSFARISEADMRAMYAYFMHGVEPVNVANKDTDIPWPLSMRWPLAFWRGIFAPTPSDFVANPQVDPVLERGRYLVEGLGHCGACHTPRSLTMQEKALSESEGDDYLAGSNAPIDGWVASSLRGENRDGLGTWSEAELAEFLKTGRNDKSVVFGGMSDVVEHSLQYLSDDDITAIARYLKSLPPRGGKQTPAPVEDSVAKDLWKGNDSKTGAALYVDNCAACHRTDGAGYKRAFPSLKGNPVVQTEDATSLIHIVLTGSTTPAVKDAVSNLTMPSFGWRLDDQQVADVVNFIRTSWGNNAPAVSASDVAKVRKETAAHDEKALGNADISKLPGAGQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Subcellular localization

Localization
Unknown

Gene Ontology (GO)

6
  • GO:0016614 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
  • GO:0009055 A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways.
  • GO:0005506 Binding to an iron (Fe) ion.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0020037 Binding to a heme, a compound composed of iron complexed in a porphyrin (tetrapyrrole) ring.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

37 records
Show feature table
Start End DB Term Name
21 156 SUPERFAMILY SSF46626 Cytochrome c
21 156 InterPro IPR036909 Cytochrome c-like domain superfamily
155 302 Gene3D G3DSA:1.10.760.10 -
155 302 InterPro IPR036909 Cytochrome c-like domain superfamily
1 136 Gene3D G3DSA:1.10.760.10 -
1 136 InterPro IPR036909 Cytochrome c-like domain superfamily
29 133 ProSiteProfiles PS51007 Cytochrome c family profile.
29 133 InterPro IPR009056 Cytochrome c-like domain
1 17 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile.
1 21 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
316 406 ProSiteProfiles PS51007 Cytochrome c family profile.
316 406 InterPro IPR009056 Cytochrome c-like domain
177 293 ProSiteProfiles PS51007 Cytochrome c family profile.
177 293 InterPro IPR009056 Cytochrome c-like domain
1 26 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
303 432 Gene3D G3DSA:1.10.760.10 -
303 432 InterPro IPR036909 Cytochrome c-like domain superfamily
22 446 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
327 338 PRINTS PR00605 Class IC cytochrome C signature
327 338 InterPro IPR008168 Cytochrome c, class IC
380 402 PRINTS PR00605 Class IC cytochrome C signature
380 402 InterPro IPR008168 Cytochrome c, class IC
1 439 PIRSF PIRSF000018 Mb_ADH_cytochrome_c
1 439 InterPro IPR014353 Membrane-bound alcohol dehydrogenase, cytochrome c subunit
6 17 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
320 426 SUPERFAMILY SSF46626 Cytochrome c
320 426 InterPro IPR036909 Cytochrome c-like domain superfamily
7 425 PANTHER PTHR35008 BLL4482 PROTEIN-RELATED
1 21 Phobius SIGNAL_PEPTIDE Signal peptide region
318 402 Pfam PF13442 Cytochrome C oxidase, cbb3-type, subunit III
318 402 InterPro IPR009056 Cytochrome c-like domain
31 128 Pfam PF13442 Cytochrome C oxidase, cbb3-type, subunit III
31 128 InterPro IPR009056 Cytochrome c-like domain
180 298 SUPERFAMILY SSF46626 Cytochrome c
180 298 InterPro IPR036909 Cytochrome c-like domain superfamily
18 21 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.

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
0.998
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Surrounding area
Pocket 2 P2Rank #2
0.93
Likely same site as FPocket 12 0.8 Å 24 shared residues 96% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.358
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Surrounding area
Pocket 4 P2Rank #4
0.116
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Surrounding area
Pocket 5 P2Rank #5
0.094
Likely same site as FPocket 27 7.7 Å 10 shared residues 77% of smaller site
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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
0.97 Unusual size
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Surrounding area
Pocket 2 FPocket #12
0.934
Likely same site as P2Rank 2 0.8 Å 24 shared residues 96% of smaller site
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Surrounding area
Pocket 3 FPocket #9
0.844 Unusual size
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Surrounding area
Pocket 4 FPocket #27
0.294 Unusual size
Likely same site as P2Rank 5 7.7 Å 10 shared residues 77% of smaller site
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Surrounding area
Residue sets
UniProt: Binding site:192-192 covalent
UniProt: Binding site:195-195 covalent
UniProt: Binding site:196-196 axial binding residue
UniProt: Binding site:329-329 covalent
UniProt: Binding site:332-332 covalent
UniProt: Binding site:333-333 axial binding residue
UniProt: Binding site:43-43 covalent
UniProt: Binding site:46-46 covalent
UniProt: Binding site:47-47 axial binding residue
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_A0A0H3GZ84
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_05311
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GZ84