KpKP13 Protein target profile

Capsule assembly 55.8 kDa protein in cps region

Accession: KP13_03809

Gene: AHE43654.1 wzi 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GSK2

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Length 477

Pocket druggability (P2Rank · AlphaFold DB model) 0.968

Direct ligand evidence 0 49 total records

Functional annotation 0 EC 0 GO

Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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 0.97, FPocket 0.95). 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 0.95. This is a computational pocket signal, not binding validation. 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: 0.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 47.257 Higher values support similarity to known essential genes.
DEG E-value: 3.2e-147 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 93.72 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) 0.968

Structure A0A0H3GSK2

Pocket Pocket 1

Druggability (FPocket) 0.955

Structure A0A0H3GSK2

Pocket Pocket 21

ColabFold model

P2Rank 0.962 · Pocket 1

FPocket 0.948 · Pocket 13

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 14 / 4744 genomes with a hit

Prevalence 0.3%

Cross-references

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

Sequence

UniProt A0A0H3GSK2

Sequence

Primary amino-acid sequence viewer.

MIKIARIAVTLGLLSSLGVQAYAAGLVVNDNDLRNDLAWLSDRGIIHLSLSTWPLSQEEIARALKKAKPSYSSEQVVLARINQRLSALKADFRVTGYTSTDQPGTPQGFGQTQPADNSLGLAFNNSGEWWDVHLQGNVEGGERISNGSRFNANGAYGAVKFWNQWLSFGQVPQWWGPGYEGSLIRGDAMRPMTGFLMQRAEQAAPETWWLRWVGPWQYQISASQMNQYTAVPHAKIIGGRFTFSPFQSLELGASRIMQWGGEGRPQSLSSFWDGFTGKDNTGTDNEPGNQLAGFDFKFKLEPTLGWPVSFYGQMIGEDESGYLPSANMFLGGVEGHHGWGKDAVNWYLEAHDTRTNMSRTNYSYNHHIYKDGYYQQGYPLGDAMGGDGQLVAGKVELITEDNQRWSTRIVYAKVNPENQSINKAFPHADTLKGVQLGWSGDVYQSVRLNTSLWYTNANNSDSDDVGASAGIEIPFSL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

Subcellular localization

Localization: OuterMembrane

No GO or EC annotations are currently loaded for this protein.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

13 records

Show feature table

Start	End	DB	Term	Name
1	6	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
24	477	Gene3D	G3DSA:2.40.160.130	Capsule assembly protein Wzi
24	477	InterPro	IPR038636	Capsule assembly protein Wzi superfamily
1	23	SignalP_EUK	SignalP-noTM	SignalP-noTM
7	18	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
7	29	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
24	477	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
19	23	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
89	466	Pfam	PF14052	Capsule assembly protein Wzi
89	466	InterPro	IPR026950	Capsule assembly protein Wzi
1	21	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
1	23	Phobius	SIGNAL_PEPTIDE	Signal peptide region
1	23	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM

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

0.968

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Surrounding area

Pocket 2 P2Rank #2

0.173

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Surrounding area

Pocket 3 P2Rank #3

0.076

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Surrounding area

Pocket 4 P2Rank #4

0.072

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Surrounding area

Pocket 5 P2Rank #5

0.04

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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 #21

0.955

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Surrounding area

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.962

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Surrounding area

Pocket 2 P2Rank #2

0.204

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Surrounding area

Pocket 3 P2Rank #3

0.079

Likely same site as FPocket 13 2.4 Å 10 shared residues 100% of smaller site

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Surrounding area

Pocket 4 P2Rank #4

0.059

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Surrounding area

Pocket 5 P2Rank #5

0.054

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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 #13

0.948

Likely same site as P2Rank 3 2.4 Å 10 shared residues 100% of smaller site

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Surrounding area

Pocket 2 FPocket #2

0.427

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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_A0A0H3GSK2	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_03809	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.

49 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 3 records from similar proteins

Structural ligands 3 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 46 similarity-based ZINC candidates

Best available ligand signal

D12 PDB via homolog 170.3 Da · LogP 4.93 · TPSA 0.0 Open detail RCSB PDB

HEX PDB via homolog Detail RCSB PDB

OCT PDB via homolog Detail RCSB PDB

ZINC1545440 ZINC proposed compound · Tanimoto 0.615 Detail ZINC

ZINC1644076 ZINC proposed compound · Tanimoto 0.615 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
D12 RCSB PDB	2YNK	Q8GNN6	170.3 Da LogP 4.93 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCC`
HEX RCSB PDB	2YNK	Q8GNN6	86.2 Da LogP 2.59 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCC`
OCT RCSB PDB	2YNK	Q8GNN6	114.2 Da LogP 3.37 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCCC`

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
ZINC1545440 ZINC	0.615	213.4 Da LogP 4.65 TPSA 26.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCN`
ZINC1644076 ZINC	0.615	214.4 Da LogP 4.68 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCO`
ZINC1680803 ZINC	0.615	200.4 Da LogP 4.29 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCO`
ZINC195766643 ZINC	0.615	231.9 Da LogP 2.93 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCCC[Sn+3]`
ZINC59144932 ZINC	0.615	202.4 Da LogP 4.84 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCS`
ZINC100027350 ZINC	0.571	227.4 Da LogP 4.91 TPSA 12.0	✓ Ro5	✓ Clean	`CCCCCCCCNCCCCCCC`
ZINC1627284 ZINC	0.571	214.4 Da LogP 4.94 TPSA 9.2	✓ Ro5	✓ Clean	`CCCCCCCOCCCCCCC`
ZINC1699899 ZINC	0.571	202.4 Da LogP 4.88 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCSCCCCCC`
ZINC1724011 ZINC	0.571	213.4 Da LogP 4.52 TPSA 12.0	✓ Ro5	✓ Clean	`CCCCCCCNCCCCCCC`
ZINC2564179 ZINC	0.571	214.4 Da LogP 4.94 TPSA 9.2	✓ Ro5	✓ Clean	`CCCCCCCCOCCCCCC`
ZINC100050955 ZINC	0.533	327.6 Da LogP 4.48 TPSA 36.1	✓ Ro5	✓ Clean	`CCCCCCCCNCCNCCNCCCCCCCC`
ZINC100077022 ZINC	0.533	227.4 Da LogP 4.86 TPSA 3.2	✓ Ro5	✓ Clean	`CCCCCCCN(C)CCCCCCC`
ZINC100924963 ZINC	0.533	284.5 Da LogP 4.89 TPSA 24.1	✓ Ro5	✓ Clean	`CCCCCCCCNCCNCCCCCCCC`
ZINC106401282 ZINC	0.533	227.4 Da LogP 4.91 TPSA 12.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCNC`
ZINC1673414 ZINC	0.533	228.4 Da LogP 4.61 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[N+](C)(C)C`
ZINC1687260 ZINC	0.533	213.4 Da LogP 4.47 TPSA 3.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCN(C)C`
ZINC1700269 ZINC	0.533	200.4 Da LogP 3.83 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCCCCC[N+](C)(C)C`
ZINC2555244 ZINC	0.533	227.4 Da LogP 4.86 TPSA 3.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCN(C)C`
ZINC35052519 ZINC	0.533	228.4 Da LogP 3.33 TPSA 24.1	✓ Ro5	✓ Clean	`CCCCCCNCCNCCCCCC`
ZINC59359855 ZINC	0.533	231.5 Da LogP 4.79 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[S+](C)C`
ZINC100015910 ZINC	0.500	214.4 Da LogP 4.68 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCC[C@@H](O)CCCCCC`
ZINC114881475 ZINC	0.500	206.4 Da LogP 4.31 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCCCCC(S)S`
ZINC1593347 ZINC	0.500	246.5 Da LogP 4.68 TPSA 17.1	✓ Ro5	✓ Clean	`CCCCCCCS(=O)CCCCCCC`
ZINC1599570 ZINC	0.500	227.4 Da LogP 4.86 TPSA 3.2	✓ Ro5	✓ Clean	`CCCCCN(CCCCC)CCCCC`
ZINC1605994 ZINC	0.500	202.4 Da LogP 4.88 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCCCCCSCC`
ZINC1606032 ZINC	0.500	200.4 Da LogP 4.29 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCC[C@@H](O)CCCCC`
ZINC1606040 ZINC	0.500	214.4 Da LogP 4.68 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCC[C@@H](O)CCCCC`
ZINC1606049 ZINC	0.500	200.4 Da LogP 4.29 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCC(O)CCCCCC`
ZINC1672455 ZINC	0.500	226.4 Da LogP 4.07 TPSA 34.1	✓ Ro5	Alert	`CCCCCCC(=O)C(=O)CCCCCC`
ZINC1687262 ZINC	0.500	213.4 Da LogP 4.52 TPSA 12.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNCC`
ZINC1693894 ZINC	0.500	212.4 Da LogP 4.89 TPSA 17.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC=O`
ZINC1697133 ZINC	0.500	214.4 Da LogP 4.94 TPSA 9.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCC`
ZINC169808442 ZINC	0.500	305.1 Da LogP 4.57 TPSA 17.1	✓ Ro5	✓ Clean	`CCCCCC[Sn](=O)CCCCCC`
ZINC196468891 ZINC	0.500	261.0 Da LogP 3.91 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCC[Sn+2]CCCCC`
ZINC20231719 ZINC	0.500	234.4 Da LogP 3.56 TPSA 34.1	✓ Ro5	✓ Clean	`CCCCCCS(=O)(=O)CCCCCC`
ZINC2166283 ZINC	0.500	262.5 Da LogP 4.34 TPSA 34.1	✓ Ro5	✓ Clean	`CCCCCCCCS(=O)(=O)CCCCCC`
ZINC221753674 ZINC	0.500	324.3 Da LogP 4.61 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCC[Sn](Cl)(Cl)Cl`
ZINC2508105 ZINC	0.500	200.4 Da LogP 4.29 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCC[C@H](O)CCCCC`
ZINC2509968 ZINC	0.500	214.4 Da LogP 4.68 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCC[C@H](O)CCCCCC`
ZINC2528299 ZINC	0.500	214.4 Da LogP 4.68 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCC[C@H](O)CCCCC`
ZINC2900787 ZINC	0.500	228.4 Da LogP 4.61 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCCCC[N+](CC)(CC)CC`
ZINC45331803 ZINC	0.500	201.4 Da LogP 3.80 TPSA 35.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCON`
ZINC59631801 ZINC	0.500	200.4 Da LogP 3.37 TPSA 38.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNN`
ZINC60107866 ZINC	0.500	242.5 Da LogP 4.41 TPSA 24.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNNCCC`
ZINC71773056 ZINC	0.500	200.4 Da LogP 3.32 TPSA 29.3	✓ Ro5	✓ Clean	`CCCCCCN(N)CCCCCC`
ZINC97973035 ZINC	0.500	212.4 Da LogP 4.23 TPSA 49.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=N)N`

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.