KpKP13 Protein target profile

Oxaloacetate decarboxylase beta chain

Accession: KP13_31779

Gene: AHE42446.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GJ14
Length 415
Pocket druggability (P2Rank · AlphaFold DB model) 0.427
Direct ligand evidence 0 51 total records
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.

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
32.5% 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
92.36 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) 0.427
Structure A0A0H3GJ14
Pocket Pocket 1
Druggability (FPocket) 0.824
Structure A0A0H3GJ14
Pocket Pocket 25
ColabFold model
P2Rank 0.845 · Pocket 1
FPocket 0.956 · Pocket 11
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 1543 / 4744 genomes with a hit
Prevalence 32.5%

Sequence

Primary amino-acid sequence viewer.

MESLNALIQGMGLMHLGAGQAVMLLVSLLLLWLAIAKKFEPLLLLPIGFGGLLSNIPEAGLALTALESLLAHHDPAQLAVIAAKLHCAPDVHAIKEALALALPSVQGQMESLAVDMGYSAGVLAIFYKVAIGSGIAPLVIFMGVGAMTDFGPLLANPRTLLLGAAAQFGIFATVLGALTLNYFGIISFTLPQAAAIGIIGGADGPTAIYLSGKLAPELLGAIAVAAYSYMALVPLIQPPIMKALTTDKERKIRMVQLRTVSKREKILFPAVLLLLVALLLPDAAPLLGMFCFGNLMRESGVVERLSDTVQNALINIVTIFLGLSVGAKLVADKFLQPQTLGILVLGVIAFCVGTAAGVLMAKLMNVFSRHKINPLIGSAGVSAVPMAARVSNKVGLEADGQNFLLMHAMGPNVAG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization
CytoplasmicMembrane

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
  • GO:0006814 The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0015451 Primary active transport of a solute across a membrane driven by decarboxylation of a cytoplasmic substrate. Primary active transport is catalysis of the transport of a solute across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by a primary energy source.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

34 records
Show feature table
Start End DB Term Name
122 144 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
13 35 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
159 178 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
266 288 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
42 66 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
67 124 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
217 236 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 415 PIRSF PIRSF015658 MmdB_OadB
1 415 InterPro IPR005661 Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, beta subunit
20 415 Pfam PF03977 Na+-transporting oxaloacetate decarboxylase beta subunit
20 415 InterPro IPR005661 Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, beta subunit
180 202 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
12 35 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
237 265 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
125 147 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
339 361 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
331 341 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
36 41 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 415 PANTHER PTHR35806 OXALOACETATE DECARBOXYLASE BETA CHAIN 2
148 158 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
19 415 NCBIfam TIGR01109 sodium ion-translocating decarboxylase subunit beta
19 415 InterPro IPR005661 Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, beta subunit
214 236 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
312 330 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
184 202 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
308 327 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
293 311 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
203 213 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
266 292 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
342 361 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
362 415 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
179 183 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
159 178 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.

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
0.427
Likely same site as FPocket 6 4.2 Å 15 shared residues 100% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.265
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Surrounding area
Pocket 3 P2Rank #3
0.105
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Surrounding area
Pocket 4 P2Rank #4
0.105
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Surrounding area
Pocket 5 P2Rank #5
0.094
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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 #25
0.824
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Surrounding area
Pocket 2 FPocket #6
0.697
Likely same site as P2Rank 1 4.2 Å 15 shared residues 100% of smaller site
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Surrounding area
Pocket 3 FPocket #3
0.407
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Surrounding area
Pocket 4 FPocket #14
0.203
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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_A0A0H3GJ14
AlphaFold DB full sequence Viewing
ColabFold KP13_31779
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.

51 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 1 records from similar proteins
Structural ligands 1 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
LMT PDB via homolog 510.6 Da · LogP -0.45 · TPSA 178.5 Open detail RCSB PDB
ZINC100053689 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC100053691 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC1501015302 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC2039285652 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

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
LMT RCSB PDB Q8ZRY4 510.6 Da LogP -0.45 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1…

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.