Protein target profile

VK055_1212

intracellular septation protein A

Genome: KpATCC43816 Gene: ispZ AIK79835.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GNA1

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Length 179

Pocket druggability 0.972

Functional annotation 0 EC 2 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: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.97, P2Rank 0.85). 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

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: 2.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 92.179 Higher values support similarity to known essential genes.
DEG E-value: 1.12e-120 Smaller values mean stronger essential-gene similarity.

Localization

Localization: CytoplasmicMembrane

Structure confidence

ColabFold pLDDT: 90.96 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.972

Structure A0A0H3GNA1

Pocket Pocket 6

P2Rank 0.855

Structure A0A0H3GNA1

Pocket Pocket 1

ColabFold model

FPocket 0.968 · Pocket 6

P2Rank 0.873 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 122 / 4744 genomes with a hit

Prevalence 2.6%

Cross-references

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

Sequence

UniProt A0A0H3GNA1

Sequence

Primary amino-acid sequence viewer.

MKQFLDFLPLVVFFAFYKLYDIYAATTALIVATAVVLIYSWVRYRKVEKMALITFVLVAVFGGLTIFFHNDEFIKWKVTVIYALFAGALLFSQWVMKKPLIQRMLGKELSLPQQVWSRLNLAWAVFFILCGLANIYIAFWLPQNIWVNFKVFGLTALTLVFTLLSGIYIYRHMPQDDHH

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
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.

24 records

Show feature table

Start	End	DB	Term	Name
51	68	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
1	19	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
20	42	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
151	170	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
151	170	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
40	50	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1	176	Hamap	MF_00189	Membrane-spanning protein YciB [yciB].
1	176	InterPro	IPR006008	Inner membrane-spanning protein YciB
140	150	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
171	179	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
117	139	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
69	73	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	175	Pfam	PF04279	Intracellular septation protein A
1	175	InterPro	IPR006008	Inner membrane-spanning protein YciB
97	116	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1	177	NCBIfam	TIGR00997	septation protein IspZ
1	177	InterPro	IPR006008	Inner membrane-spanning protein YciB
20	39	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
74	96	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
78	95	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
119	141	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
1	178	PANTHER	PTHR36917	INTRACELLULAR SEPTATION PROTEIN A-RELATED
1	178	InterPro	IPR006008	Inner membrane-spanning protein YciB
51	68	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 · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #6

0.972

Likely same site as P2Rank 1 7.8 Å 12 shared residues 80% of smaller site

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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1

0.855

Likely same site as FPocket 6 7.8 Å 12 shared residues 80% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.046

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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_A0A0H3GNA1	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_1212	ColabFold	—	—	full sequence	—	Loaded