Protein target profile

VK055_0268

yceI-like domain protein

Genome: KpATCC43816 Gene: AIK78894.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0G3N6R1

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Length 192

Pocket druggability 1

Direct ligand evidence 0 58 total records

Functional annotation 0 EC 0 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 0.99. 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: 0.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 35.979 Higher values support similarity to known essential genes.

Localization

Localization: Unknown

Structure confidence

ColabFold pLDDT: 93.72 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 1

Structure A0A0G3N6R1

Pocket Pocket 1

P2Rank 0.991

Structure A0A0G3N6R1

Pocket Pocket 1

ColabFold model

FPocket 1 · Pocket 1

P2Rank 0.991 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 18 / 4744 genomes with a hit

Prevalence 0.4%

Cross-references

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

Sequence

UniProt A0A0G3N6R1

Sequence

Primary amino-acid sequence viewer.

MNTLKKTALLSVLALYIPVSQAAAKEYSLDPQHTSVVISWNHFGFSNPTAYIYDVSGKLAFDKESPEKSSVNVTLPVKTIDAHVKALTDEFLGKEYFDVKTFPDATFQSTKVESKGDNKYDVEGNLTIKGITKPVVLHAVLNKQDMHPMVKKEAIGFDATGVIKRSDFKLDKYVPAVSDNVTITLSTEAYAK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

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.

17 records

Show feature table

Start	End	DB	Term	Name
23	192	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	24	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
24	190	SUPERFAMILY	SSF101874	YceI-like
24	190	InterPro	IPR036761	Lipid/polyisoprenoid-binding, YceI-like superfamily
1	22	Phobius	SIGNAL_PEPTIDE	Signal peptide region
25	192	Gene3D	G3DSA:2.40.128.110	-
25	192	InterPro	IPR036761	Lipid/polyisoprenoid-binding, YceI-like superfamily
1	22	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
7	17	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
8	190	PANTHER	PTHR34406	PROTEIN YCEI
1	24	SignalP_EUK	SignalP-noTM	SignalP-noTM
26	190	SMART	SM00867	YceI_2
26	190	InterPro	IPR007372	Lipid/polyisoprenoid-binding, YceI-like
18	22	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	6	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
27	189	Pfam	PF04264	YceI-like domain
27	189	InterPro	IPR007372	Lipid/polyisoprenoid-binding, YceI-like

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 #1

1.0

Likely same site as P2Rank 1 0.5 Å 44 shared residues 96% of smaller site

Unusual size

Show in viewer

Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1

0.991

Likely same site as FPocket 1 0.5 Å 44 shared residues 96% of smaller site

Show in viewer

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_A0A0G3N6R1	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_0268	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.

58 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 8 records from similar proteins

Structural ligands 8 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

8PP PDB via homolog 639.1 Da · LogP 14.99 · TPSA 20.2 Open detail RCSB PDB

9UM PDB via homolog Detail RCSB PDB

LFA PDB via homolog Detail RCSB PDB

MBO PDB via homolog Detail RCSB PDB

MNB PDB via homolog Detail RCSB PDB

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
8PP RCSB PDB	1Y0G	P0A8X2	639.1 Da LogP 14.99 TPSA 20.2	2 viol.	✓ Clean	`CC(=CCCC(=CCC/C(=C/CC/C(=C/CCC(=CCC/C(=C/CCC(=C…`
9UM RCSB PDB	5W30	Q0PB90	271.1 Da LogP 1.02 TPSA 43.0	✓ Ro5	✓ Clean	`CC1=C(N2C(=C(C(=O)N2C1=O)C)CBr)C`
LFA RCSB PDB	5W17	Q0PB90	282.6 Da LogP 8.05 TPSA 0.0	1 viol.	✓ Clean	`CCCCCCCCCCCCCCCCCCCC`
MBO RCSB PDB	5W31	Q0PB90	321.7 Da LogP 0.56 TPSA 37.3	✓ Ro5	✓ Clean	`c1cc(ccc1C(=O)O)[Hg]`
MNB RCSB PDB	5W2Z	Q0PB90	199.2 Da LogP 1.58 TPSA 80.4	✓ Ro5	✓ Clean	`c1cc(c(cc1S)C(=O)O)[N+](=O)[O-]`
OTP RCSB PDB	1WUB	P83815	722.9 Da LogP 13.26 TPSA 113.3	2 viol.	✓ Clean	`CC(=CCC/C(=C/CC/C(=C/CC/C(=C/CC/C(=C/CC/C(=C/CC…`
SEC RCSB PDB	5W2V	Q0PB90	168.1 Da LogP -1.28 TPSA 63.3	✓ Ro5	✓ Clean	`C([C@@H](C(=O)O)N)[SeH]`
UQ8 RCSB PDB	7BWL	Q9I690	727.1 Da LogP 14.40 TPSA 52.6	2 viol.	Alert	`CC1=C(C(=O)C(=C(C1=O)OC)OC)CC=C(C)CC\C=C(/C)\CC…`

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
ZINC1532641 ZINC	0.972	318.4 Da LogP 4.04 TPSA 52.6	✓ Ro5	Alert	`COC1=C(OC)C(=O)C(C/C=C(\C)CCC=C(C)C)=C(C)C1=O`
ZINC1559692 ZINC	0.730	250.3 Da LogP 2.32 TPSA 52.6	✓ Ro5	Alert	`COC1=C(OC)C(=O)C(CC=C(C)C)=C(C)C1=O`
ZINC8215740 ZINC	0.697	246.1 Da LogP 1.18 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCO[P@@](=O)(O)OP(=O)(O)O`
ZINC1531959 ZINC	0.676	246.3 Da LogP 4.33 TPSA 40.5	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/Cc1cc(O)ccc1O`
ZINC71769106 ZINC	0.657	326.1 Da LogP 1.30 TPSA 159.8	✓ Ro5	✓ Clean	`CC(C)=CCO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O`
ZINC2575270 ZINC	0.656	211.1 Da LogP 0.99 TPSA 117.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC4404106 ZINC	0.656	212.1 Da LogP 1.20 TPSA 123.6	✓ Ro5	✓ Clean	`O=C(O)c1cc([N+](=O)[O-])ccc1[N+](=O)[O-]`
ZINC2565533 ZINC	0.655	256.1 Da LogP 0.90 TPSA 160.9	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(=O)O)c([N+](=O)[O-])cc1[N+](=O)[O-]`
ZINC2553928 ZINC	0.643	207.2 Da LogP -0.42 TPSA 69.0	✓ Ro5	✓ Clean	`Cc1c(C)n2c(CN)c(C)c(=O)n2c1=O`
ZINC8436838 ZINC	0.639	262.1 Da LogP 0.15 TPSA 133.5	✓ Ro5	✓ Clean	`C/C(=C\CO[P@@](=O)(O)OP(=O)(O)O)CO`
ZINC1689765 ZINC	0.636	201.6 Da LogP 1.95 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(Cl)ccc1[N+](=O)[O-]`
ZINC1692553 ZINC	0.636	246.0 Da LogP 2.06 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(Br)ccc1[N+](=O)[O-]`
ZINC34143793 ZINC	0.636	293.0 Da LogP 1.90 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(I)ccc1[N+](=O)[O-]`
ZINC114185151 ZINC	0.632	298.2 Da LogP 2.15 TPSA 108.7	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC13539354 ZINC	0.615	332.2 Da LogP 3.20 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C(\F)CO[P@](=O)(O)OP(=O)(O)O`
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`
ZINC134079 ZINC	0.600	242.2 Da LogP 2.75 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)cc2)cc1`
ZINC1640789 ZINC	0.600	374.3 Da LogP 3.55 TPSA 108.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccc(C(=O)c3ccc(C(=O)O)cc3)cc…`
ZINC19801481 ZINC	0.600	223.2 Da LogP 2.59 TPSA 80.4	✓ Ro5	✓ Clean	`CC(C)(C)c1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC2146859 ZINC	0.600	270.2 Da LogP 2.31 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC3147211 ZINC	0.600	318.3 Da LogP 4.42 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccc(C(=O)O)cc3)cc2)cc1`
ZINC188555 ZINC	0.591	350.3 Da LogP 4.67 TPSA 93.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(Oc3ccc(C(=O)O)cc3)cc2)cc1`
ZINC241160 ZINC	0.591	258.2 Da LogP 2.88 TPSA 83.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(C(=O)O)cc2)cc1`
ZINC1870293 ZINC	0.583	247.1 Da LogP 0.10 TPSA 138.0	✓ Ro5	✓ Clean	`O=C(O)c1cc(P(=O)(O)O)ccc1[N+](=O)[O-]`
ZINC197020550 ZINC	0.583	246.2 Da LogP -0.06 TPSA 140.6	✓ Ro5	✓ Clean	`NS(=O)(=O)c1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC19845324 ZINC	0.583	210.2 Da LogP 1.36 TPSA 83.7	✓ Ro5	✓ Clean	`CN(C)c1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC59269089 ZINC	0.583	245.2 Da LogP 0.70 TPSA 114.6	✓ Ro5	✓ Clean	`CS(=O)(=O)c1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC72338575 ZINC	0.583	235.1 Da LogP 2.31 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(F)(F)F)ccc1[N+](=O)[O-]`
ZINC7814925 ZINC	0.583	213.2 Da LogP 2.01 TPSA 80.4	✓ Ro5	✓ Clean	`CSc1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC3845121 ZINC	0.576	226.1 Da LogP 0.57 TPSA 143.8	✓ Ro5	✓ Clean	`Nc1cc([N+](=O)[O-])c(C(=O)O)cc1C(=O)O`
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`
ZINC4284655 ZINC	0.568	224.2 Da LogP 1.25 TPSA 109.5	✓ Ro5	✓ Clean	`CC(=O)Nc1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC389804 ZINC	0.565	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(O)cc2)cc1`
ZINC392302 ZINC	0.560	230.2 Da LogP 2.88 TPSA 66.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(O)cc2)cc1`
ZINC346060 ZINC	0.559	245.6 Da LogP 1.64 TPSA 117.7	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(=O)O)c([N+](=O)[O-])cc1Cl`
ZINC14985550 ZINC	0.553	225.2 Da LogP 1.08 TPSA 106.7	✓ Ro5	✓ Clean	`COC(=O)c1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC15443713 ZINC	0.553	236.2 Da LogP 1.89 TPSA 83.7	✓ Ro5	✓ Clean	`O=C(O)c1cc(N2CCCC2)ccc1[N+](=O)[O-]`
ZINC1610707 ZINC	0.553	269.3 Da LogP 3.46 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(/C=C/c2ccccc2)ccc1[N+](=O)[O-]`
ZINC19400583 ZINC	0.553	225.2 Da LogP 2.08 TPSA 89.7	✓ Ro5	✓ Clean	`CC(C)Oc1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC22163863 ZINC	0.553	259.2 Da LogP 3.09 TPSA 89.7	✓ Ro5	✓ Clean	`O=C(O)c1cc(Oc2ccccc2)ccc1[N+](=O)[O-]`
ZINC5160214 ZINC	0.553	269.3 Da LogP 3.46 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(/C=C\c2ccccc2)ccc1[N+](=O)[O-]`
ZINC388063 ZINC	0.545	201.0 Da LogP 2.15 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Br)cc1`

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.