KpKP13 Protein target profile

Thiamine biosynthesis lipoprotein apbE

Accession: KP13_00949

Gene: AHE43523.1 apbE 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GSX9
Length 350
Pocket druggability (P2Rank · AlphaFold DB model) 0.894
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
1.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
41.214 Higher values support similarity to known essential genes.
DEG E-value
5.09e-86 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
89.84 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) 0.894
Structure A0A0H3GSX9
Pocket Pocket 1
Druggability (FPocket) 0.49
Structure A0A0H3GSX9
Pocket Pocket 3
ColabFold model
P2Rank 0.837 · Pocket 1
FPocket 0.61 · Pocket 5
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 79 / 4744 genomes with a hit
Prevalence 1.7%

Sequence

Primary amino-acid sequence viewer.

MDMTFFRAALLGACVLLSGCDSATTPATPTATATVLDGKTMGTFWRVSVIGVDEAKAQALRAKVQAQLDADDRLLSTWKNDSALMRFNHAATTEPWPVSEAMADIVTLSLRIGAKTHGAMDITVGPLVNLWGFGPDKQPVTTPDAEAIAAAKARTGLQHLQVINQSGRQFLQKDIPDLFVDLSTVGEGYAADHLARLMEQEGISRYLVSVGGALVSRGMNGEGKPWRVAIQKPTDRENAVQAIVDINGHGISTSGSYRNYYELDGKRISHVIDPQTGQPITHKLVSVTVIAPTALEADGWDTGLMVLGPEKAQQVVREEGLAVYMIVKEGEGFKTWMSPQFRTFLVGEKN

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:0017013 The addition of a flavin group to a protein amino acid.
  • 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:0046872 Binding to a metal ion.
  • GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
7 344 PANTHER PTHR30040 THIAMINE BIOSYNTHESIS LIPOPROTEIN APBE
7 344 InterPro IPR024932 Flavin transferase ApbE
1 23 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
1 7 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
25 347 FunFam G3DSA:3.10.520.10:FF:000001 FAD:protein FMN transferase
18 22 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
8 17 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
3 346 PIRSF PIRSF006268 ApbE
3 346 InterPro IPR024932 Flavin transferase ApbE
1 20 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile.
23 350 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
22 350 Gene3D G3DSA:3.10.520.10 -
22 350 InterPro IPR003374 ApbE-like superfamily
1 22 SignalP_EUK SignalP-noTM SignalP-noTM
1 23 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
41 324 Pfam PF02424 ApbE family
41 324 InterPro IPR024932 Flavin transferase ApbE
35 345 SUPERFAMILY SSF143631 ApbE-like
35 345 InterPro IPR003374 ApbE-like superfamily
1 22 Phobius SIGNAL_PEPTIDE Signal peptide region

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
0.894
Likely same site as FPocket 3 6.8 Å 11 shared residues 92% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.086
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Surrounding area
Pocket 3 P2Rank #3
0.053
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Surrounding area
Pocket 4 P2Rank #4
0.021
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Surrounding area
Pocket 5 P2Rank #5
0.017
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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
0.49
Likely same site as P2Rank 1 6.8 Å 11 shared residues 92% of smaller site
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Surrounding area
Pocket 2 FPocket #4
0.213
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Surrounding area
Residue sets
UniProt: Binding site:119-121
UniProt: Binding site:181-181
UniProt: Binding site:184-184
UniProt: Binding site:187-187
UniProt: Binding site:272-272
UniProt: Binding site:298-298
UniProt: Binding site:302-302
UniProt: Binding site:41-41
UniProt: Binding site:78-78
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_A0A0H3GSX9
AlphaFold DB full sequence Viewing
ColabFold KP13_00949
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
ADN PDB via homolog 267.2 Da · LogP -1.98 · TPSA 139.5 Open detail RCSB PDB
ZINC2047403 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC2047673 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC2169830 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC3201876 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
ADN RCSB PDB O83774 267.2 Da LogP -1.98 TPSA 139.5 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.