KpKP13 Protein target profile

Thiamine biosynthesis lipoprotein apbE

Accession: KP13_01188

Gene: AHE44771.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GSZ5

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Length 316

Pocket druggability (P2Rank · AlphaFold DB model) 0.944

Direct ligand evidence 0 51 total records

Functional annotation 1 EC 3 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

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. Second pocket predictor agrees P2Rank predicted binding-site probability 0.94. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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: 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: 95.6 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) 0.944

Structure A0A0H3GSZ5

Pocket Pocket 1

Druggability (FPocket) 0.381

Structure A0A0H3GSZ5

Pocket Pocket 18

ColabFold model

P2Rank 0.924 · Pocket 1

FPocket 0.638 · Pocket 2

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 42 / 4744 genomes with a hit

Prevalence 0.9%

Sequence

Primary amino-acid sequence viewer.

MSDNRVYSYSAVLMGSPILLKLCSHDEAMASRVFQLIKRYEDLLTVNRAESQVMDINHAAGRHPVTVSRPVFQLIQCAKAASMVRDSAFNLAIGPLVKLWRIGFHGHSVPDAAEIRARLALTRPQEVILDEATCSVFLQQPGMELDLGAIAKGYIADRVRDYLRQQQVEKALINLGGNVHTLGEWAIGLKKPFADAQALIGSLTVNGQSVVTSGTYERYFEQDGKRWHHILDPRSGYPLDNELDSVTVISADSLDGDIWTTLLFGLGVEKGCAALRQRQDIDAIFVTKNRDIILSSPQRLRFAPLDSGYRVIDCTA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Subcellular localization

Localization: Unknown

Enzyme Commission (EC)

2.7.1.180

Gene Ontology (GO)

GO:0017013 The addition of a flavin group to a protein amino acid.
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.

10 records

Show feature table

Start	End	DB	Term	Name
6	295	PANTHER	PTHR30040	THIAMINE BIOSYNTHESIS LIPOPROTEIN APBE
6	295	InterPro	IPR024932	Flavin transferase ApbE
14	285	Pfam	PF02424	ApbE family
14	285	InterPro	IPR024932	Flavin transferase ApbE
2	312	Gene3D	G3DSA:3.10.520.10	-
2	312	InterPro	IPR003374	ApbE-like superfamily
1	304	PIRSF	PIRSF006268	ApbE
1	304	InterPro	IPR024932	Flavin transferase ApbE
6	296	SUPERFAMILY	SSF143631	ApbE-like
6	296	InterPro	IPR003374	ApbE-like superfamily

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

0.944

Likely same site as FPocket 18 4.1 Å 32 shared residues 94% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.127

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Surrounding area

Pocket 3 P2Rank #3

0.088

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Surrounding area

Pocket 4 P2Rank #4

0.018

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Surrounding area

Pocket 5 P2Rank #5

0.001

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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 #18

0.381 Unusual size

Likely same site as P2Rank 1 4.1 Å 32 shared residues 94% of smaller site

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Surrounding area

Pocket 2 FPocket #2

0.213

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Surrounding area

Residue sets

UniProt: Binding site:149-149

UniProt: Binding site:257-257

UniProt: Binding site:261-261

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1

0.924

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Surrounding area

Pocket 2 P2Rank #2

0.184

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Surrounding area

Pocket 3 P2Rank #3

0.141

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Surrounding area

Pocket 4 P2Rank #4

0.013

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Surrounding area

Pocket 5 P2Rank #5

0.0

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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_A0A0H3GSZ5	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_01188	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

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ADN RCSB PDB	4XDR	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)…`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC2047403 ZINC	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H]1O`
ZINC2047673 ZINC	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@@H]1O`
ZINC2169830 ZINC	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O`
ZINC3201876 ZINC	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC3201878 ZINC	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC3830178 ZINC	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@H]1O`
ZINC3830179 ZINC	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@H]1O`
ZINC3978047 ZINC	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@H]1O`
ZINC3978048 ZINC	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@H](O)[C@H]1O`
ZINC3978049 ZINC	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H]1O`
ZINC4048240 ZINC	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@H]1O`
ZINC8580514 ZINC	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H]1O`
ZINC895113 ZINC	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@@H]1O`
ZINC896706 ZINC	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@H]1O`
ZINC970363 ZINC	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC4188096 ZINC	0.974	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](…`
ZINC4188103 ZINC	0.974	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC4188112 ZINC	0.974	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](…`
ZINC4188116 ZINC	0.974	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC101227935 ZINC	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H]1N`
ZINC1868288 ZINC	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1N`
ZINC39294072 ZINC	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H]1N`
ZINC53204366 ZINC	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1N`
ZINC57675642 ZINC	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@H]1N`
ZINC57675644 ZINC	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@H]1N`
ZINC57675648 ZINC	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H]1N`
ZINC57675649 ZINC	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC71250611 ZINC	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@@H]1N`
ZINC4809089 ZINC	0.833	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](S)[C@H]1O`
ZINC4809090 ZINC	0.833	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](S)[C@H]1O`
ZINC4809091 ZINC	0.833	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](S)[C@@H]1O`
ZINC4809092 ZINC	0.833	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](S)[C@@H]…`
ZINC5139067 ZINC	0.829	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CS)[C@@H](O)[C@H]1O`
ZINC105358492 ZINC	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H]1F`
ZINC22805 ZINC	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1F`
ZINC2383767290 ZINC	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@@H]1F`
ZINC3827883 ZINC	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@H]1F`
ZINC5163038 ZINC	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1F`
ZINC5372462 ZINC	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC66155300 ZINC	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H]1F`
ZINC83323919 ZINC	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@@H]1F`
ZINC13470207 ZINC	0.814	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](N)[C@H]1O`
ZINC14418140 ZINC	0.814	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](N)[C@H]1O`
ZINC79682926 ZINC	0.814	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](N)[C@@H]1O`
ZINC3814316 ZINC	0.810	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]…`
ZINC4773848 ZINC	0.810	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]…`
ZINC4773849 ZINC	0.810	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H…`
ZINC4773850 ZINC	0.810	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@H…`
ZINC4773851 ZINC	0.810	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@…`
ZINC77981211 ZINC	0.810	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H]…`

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.

Sequence

UniProt A0A0H3GSZ5