Protein target profile

VK055_0478

cfa

Genome: KpATCC43816 Gene: AIK79101.1 cfa 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQT4

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Length 382

Pocket druggability 1

Direct ligand evidence 0 57 total records

Functional annotation 0 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 1.00. 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: 3.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 35.0 Higher values support similarity to known essential genes.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 92.6 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 A0A0H3GQT4

Pocket Pocket 1

P2Rank 0.997

Structure A0A0H3GQT4

Pocket Pocket 1

ColabFold model

FPocket 0.993 · Pocket 2

P2Rank 0.997 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 146 / 4744 genomes with a hit

Prevalence 3.1%

Cross-references

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

Sequence

UniProt A0A0H3GQT4

Sequence

Primary amino-acid sequence viewer.

MSSSCIEEVSVPNDDWYRIAAELLGRAGIEINGSAPSDLRVKNPLFFKRVLQEGSLGLGESYMDGWWECERLDIFFHKVLRAGLEKQLPHHFKDTLRIAGARLFNLQSKKRAWIVGKEHYDLGNDLFSRMLDPYMQYSCGYWKEAQSLEAAQQAKLDLICRKLELEPGMRVLDIGCGWGGLAEYMARNYQVSVVGVTISAEQQKMAQARCADLDVEIRLQDYRDLHDSFDRIVSVGMFEHVGPKNYATYFEVADRNLKPNGRFLLHTIGSKVTDHNVDPWIDKYIFPNGCLPSVRHIAEASEKHFVMEDWHNFGADYDTTLMAWYERFLASWPEIADNYSERFKRMFTYYLNACAGAFRARDIQLWQVVFSRGIEHGLRVAR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0008610 The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
GO:0032259 The process in which a methyl group is covalently attached to a molecule.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

9 records

Show feature table

Start	End	DB	Term	Name
105	372	Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39
105	372	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
117	373	SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases
117	373	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
170	266	CDD	cd02440	AdoMet_MTases
39	373	PANTHER	PTHR43667	CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE
2	381	PIRSF	PIRSF003085	CmaB
2	381	InterPro	IPR003333	Cyclopropane mycolic acid synthase
108	368	Pfam	PF02353	Mycolic acid cyclopropane synthetase

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 2.4 Å 61 shared residues 85% of smaller site

Unusual size

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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

0.997

Likely same site as FPocket 1 2.4 Å 61 shared residues 85% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.578

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Surrounding area

Site 3 P2Rank #3

0.072

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Surrounding area

Site 4 P2Rank #4

0.01

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Surrounding area

Residue sets

UniProt: Active site:354-354

Binding pockets · FPocket

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

Site 1 FPocket #2

0.993

Likely same site as P2Rank 1 6.5 Å 49 shared residues 89% of smaller site

Unusual size

Show in viewer

Surrounding area

Site 2 FPocket #1

0.957

Unusual size

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_A0A0H3GQT4	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_0478	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.

57 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 7 records from similar proteins

Structural ligands 7 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

10A PDB via homolog 326.6 Da · LogP 7.34 · TPSA 0.0 Open detail RCSB PDB

16A PDB via homolog Detail RCSB PDB

F2W PDB via homolog Detail RCSB PDB

F2Z PDB via homolog Detail RCSB PDB

PC 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
10A RCSB PDB	1KPH	P9WPB7	326.6 Da LogP 7.34 TPSA 0.0	1 viol.	✓ Clean	`CCCCCCCCCC[N+](C)(C)CCCCCCCCCC`
16A RCSB PDB	1KPG	P9WPB7	284.6 Da LogP 6.17 TPSA 0.0	1 viol.	✓ Clean	`CCCCCCCCCCCCCCCC[N+](C)(C)C`
F2W RCSB PDB	6GKV	Q948P7	208.3 Da LogP 0.27 TPSA 22.9	✓ Ro5	✓ Clean	`C[NH+]1CCc2cc(c(cc2C1)OC)OC`
F2Z RCSB PDB	6GKY	Q948P7	207.2 Da LogP 0.88 TPSA 47.6	✓ Ro5	✓ Clean	`COc1cc2c(cc1OC)CNC(=O)C2`
PC RCSB PDB	5WP4	Q9FR44	184.2 Da LogP -0.20 TPSA 66.8	✓ Ro5	✓ Clean	`C[N+](C)(C)CCOP(=O)(O)O`
R9T RCSB PDB	5KOK	C3SBW0	343.4 Da LogP 3.15 TPSA 49.0	✓ Ro5	✓ Clean	`COc1ccc(cc1OC)C[C@@H]2c3cc(c(cc3CCN2)OC)OC`
S9T RCSB PDB	5KOK	C3SBW0	343.4 Da LogP 3.15 TPSA 49.0	✓ Ro5	✓ Clean	`COc1ccc(cc1OC)C[C@H]2c3cc(c(cc3CCN2)OC)OC`

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
ZINC1673414 ZINC	1.000	228.4 Da LogP 4.61 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[N+](C)(C)C`
ZINC1700269 ZINC	1.000	200.4 Da LogP 3.83 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCCCCC[N+](C)(C)C`
ZINC5208833 ZINC	1.000	207.2 Da LogP 0.88 TPSA 47.6	✓ Ro5	✓ Clean	`COc1cc2c(cc1OC)CC(=O)NC2`
ZINC57530 ZINC	1.000	343.4 Da LogP 3.15 TPSA 49.0	✓ Ro5	✓ Clean	`COc1ccc(C[C@@H]2NCCc3cc(OC)c(OC)cc32)cc1OC`
ZINC57531 ZINC	1.000	343.4 Da LogP 3.15 TPSA 49.0	✓ Ro5	✓ Clean	`COc1ccc(C[C@H]2NCCc3cc(OC)c(OC)cc32)cc1OC`
ZINC1624023 ZINC	0.833	392.3 Da LogP 3.90 TPSA 39.7	✓ Ro5	✓ Clean	`COc1ccc(C[C@H]2NCCc3cc(OC)c(OC)cc32)cc1Br`
ZINC3847375 ZINC	0.833	329.4 Da LogP 2.85 TPSA 60.0	✓ Ro5	✓ Clean	`COc1ccc(C[C@H]2NCCc3cc(OC)c(OC)cc32)cc1O`
ZINC3847376 ZINC	0.833	329.4 Da LogP 2.85 TPSA 60.0	✓ Ro5	✓ Clean	`COc1ccc(C[C@@H]2NCCc3cc(OC)c(OC)cc32)cc1O`
ZINC5722010 ZINC	0.833	392.3 Da LogP 3.90 TPSA 39.7	✓ Ro5	✓ Clean	`COc1ccc(C[C@@H]2NCCc3cc(OC)c(OC)cc32)cc1Br`
ZINC1629541 ZINC	0.805	313.4 Da LogP 3.14 TPSA 39.7	✓ Ro5	✓ Clean	`COc1ccc(C[C@H]2NCCc3cc(OC)c(OC)cc32)cc1`
ZINC5811656 ZINC	0.805	313.4 Da LogP 3.14 TPSA 39.7	✓ Ro5	✓ Clean	`COc1ccc(C[C@@H]2NCCc3cc(OC)c(OC)cc32)cc1`
ZINC38622442 ZINC	0.800	373.4 Da LogP 3.16 TPSA 58.2	✓ Ro5	✓ Clean	`COc1cc2c(cc1OC)[C@@H](Cc1cc(OC)c(OC)c(OC)c1)NCC2`
ZINC38622445 ZINC	0.800	373.4 Da LogP 3.16 TPSA 58.2	✓ Ro5	✓ Clean	`COc1cc2c(cc1OC)[C@H](Cc1cc(OC)c(OC)c(OC)c1)NCC2`
ZINC112977758 ZINC	0.789	244.5 Da LogP 3.13 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCC[N+](C)(C)CCC[N+](C)(C)C`
ZINC24717722 ZINC	0.786	299.4 Da LogP 2.84 TPSA 50.7	✓ Ro5	✓ Clean	`COc1cc2c(cc1OC)[C@H](Cc1ccc(O)cc1)NCC2`
ZINC24717725 ZINC	0.786	299.4 Da LogP 2.84 TPSA 50.7	✓ Ro5	✓ Clean	`COc1cc2c(cc1OC)[C@@H](Cc1ccc(O)cc1)NCC2`
ZINC71772917 ZINC	0.786	298.4 Da LogP 2.72 TPSA 56.5	✓ Ro5	Alert	`COc1cc2c(cc1OC)[C@H](Cc1ccc(N)cc1)NCC2`
ZINC71772918 ZINC	0.786	298.4 Da LogP 2.72 TPSA 56.5	✓ Ro5	Alert	`COc1cc2c(cc1OC)[C@@H](Cc1ccc(N)cc1)NCC2`
ZINC4262569 ZINC	0.780	283.4 Da LogP 3.13 TPSA 30.5	✓ Ro5	✓ Clean	`COc1cc2c(cc1OC)[C@H](Cc1ccccc1)NCC2`
ZINC4262570 ZINC	0.780	283.4 Da LogP 3.13 TPSA 30.5	✓ Ro5	✓ Clean	`COc1cc2c(cc1OC)[C@@H](Cc1ccccc1)NCC2`
ZINC39343186 ZINC	0.756	327.4 Da LogP 2.86 TPSA 49.0	✓ Ro5	✓ Clean	`COc1ccc(C[C@@H]2NCCc3cc4c(cc32)OCO4)cc1OC`
ZINC896218 ZINC	0.750	315.4 Da LogP 2.54 TPSA 71.0	✓ Ro5	✓ Clean	`COc1ccc(C[C@@H]2NCCc3cc(OC)c(O)cc32)cc1O`
ZINC896220 ZINC	0.750	315.4 Da LogP 2.54 TPSA 71.0	✓ Ro5	✓ Clean	`COc1ccc(C[C@H]2NCCc3cc(OC)c(O)cc32)cc1O`
ZINC1530808 ZINC	0.733	202.4 Da LogP 1.96 TPSA 0.0	✓ Ro5	✓ Clean	`C[N+](C)(C)CCCCCC[N+](C)(C)C`
ZINC1532339 ZINC	0.733	258.5 Da LogP 3.52 TPSA 0.0	✓ Ro5	✓ Clean	`C[N+](C)(C)CCCCCCCCCC[N+](C)(C)C`
ZINC1730254 ZINC	0.733	216.4 Da LogP 2.35 TPSA 0.0	✓ Ro5	✓ Clean	`C[N+](C)(C)CCCCCCC[N+](C)(C)C`
ZINC1730255 ZINC	0.733	230.4 Da LogP 2.74 TPSA 0.0	✓ Ro5	✓ Clean	`C[N+](C)(C)CCCCCCCC[N+](C)(C)C`
ZINC1730256 ZINC	0.733	244.5 Da LogP 3.13 TPSA 0.0	✓ Ro5	✓ Clean	`C[N+](C)(C)CCCCCCCCC[N+](C)(C)C`
ZINC20255279 ZINC	0.721	399.5 Da LogP 4.71 TPSA 49.0	✓ Ro5	✓ Clean	`CCOc1ccc(C[C@@H]2NCCc3cc(OCC)c(OCC)cc32)cc1OCC`
ZINC20255282 ZINC	0.721	399.5 Da LogP 4.71 TPSA 49.0	✓ Ro5	✓ Clean	`CCOc1ccc(C[C@H]2NCCc3cc(OCC)c(OCC)cc32)cc1OCC`
ZINC34099128 ZINC	0.714	235.2 Da LogP 0.45 TPSA 64.6	✓ Ro5	✓ Clean	`COc1cc2c(cc1OC)CC(=O)NC(=O)C2`
ZINC5720277 ZINC	0.710	221.3 Da LogP 0.92 TPSA 47.6	✓ Ro5	✓ Clean	`COc1cc2c(cc1OC)CC(=O)NCC2`
ZINC895655 ZINC	0.696	301.3 Da LogP 2.24 TPSA 82.0	✓ Ro5	Alert	`COc1cc2c(cc1O)[C@@H](Cc1ccc(O)c(O)c1)NCC2`
ZINC895656 ZINC	0.696	301.3 Da LogP 2.24 TPSA 82.0	✓ Ro5	Alert	`COc1cc2c(cc1O)[C@H](Cc1ccc(O)c(O)c1)NCC2`
ZINC3847353 ZINC	0.681	359.5 Da LogP 4.70 TPSA 30.5	✓ Ro5	✓ Clean	`COc1cc2c(cc1OCc1ccccc1)[C@H](Cc1ccccc1)NCC2`
ZINC3847354 ZINC	0.681	359.5 Da LogP 4.70 TPSA 30.5	✓ Ro5	✓ Clean	`COc1cc2c(cc1OCc1ccccc1)[C@@H](Cc1ccccc1)NCC2`
ZINC896042 ZINC	0.674	285.3 Da LogP 2.54 TPSA 61.7	✓ Ro5	✓ Clean	`COc1cc2c(cc1O)[C@@H](Cc1ccc(O)cc1)NCC2`
ZINC896120 ZINC	0.674	285.3 Da LogP 2.54 TPSA 61.7	✓ Ro5	✓ Clean	`COc1cc2c(cc1O)[C@H](Cc1ccc(O)cc1)NCC2`
ZINC3847481 ZINC	0.673	389.5 Da LogP 4.71 TPSA 39.7	✓ Ro5	✓ Clean	`COc1cc2c(cc1OC)[C@H](Cc1ccc(OCc3ccccc3)cc1)NCC2`
ZINC3847482 ZINC	0.673	389.5 Da LogP 4.71 TPSA 39.7	✓ Ro5	✓ Clean	`COc1cc2c(cc1OC)[C@@H](Cc1ccc(OCc3ccccc3)cc1)NCC2`
ZINC3847479 ZINC	0.660	299.4 Da LogP 2.84 TPSA 50.7	✓ Ro5	✓ Clean	`COc1ccc(C[C@H]2NCCc3cc(O)c(OC)cc32)cc1`
ZINC3847480 ZINC	0.660	299.4 Da LogP 2.84 TPSA 50.7	✓ Ro5	✓ Clean	`COc1ccc(C[C@@H]2NCCc3cc(O)c(OC)cc32)cc1`
ZINC1624476 ZINC	0.644	422.3 Da LogP 3.91 TPSA 49.0	✓ Ro5	✓ Clean	`COc1cc(Br)c(C[C@H]2NCCc3cc(OC)c(OC)cc32)cc1OC`
ZINC5722513 ZINC	0.644	422.3 Da LogP 3.91 TPSA 49.0	✓ Ro5	✓ Clean	`COc1cc(Br)c(C[C@@H]2NCCc3cc(OC)c(OC)cc32)cc1OC`
ZINC208615347 ZINC	0.638	312.4 Da LogP 3.11 TPSA 56.5	✓ Ro5	Alert	`COc1cc2c(cc1OC)[C@H](CCc1ccc(N)cc1)NCC2`
ZINC208615377 ZINC	0.638	312.4 Da LogP 3.11 TPSA 56.5	✓ Ro5	Alert	`COc1cc2c(cc1OC)[C@@H](CCc1ccc(N)cc1)NCC2`
ZINC3847351 ZINC	0.638	269.3 Da LogP 2.83 TPSA 41.5	✓ Ro5	✓ Clean	`COc1cc2c(cc1O)[C@H](Cc1ccccc1)NCC2`
ZINC3847352 ZINC	0.638	269.3 Da LogP 2.83 TPSA 41.5	✓ Ro5	✓ Clean	`COc1cc2c(cc1O)[C@@H](Cc1ccccc1)NCC2`
ZINC2011314 ZINC	0.630	297.4 Da LogP 3.52 TPSA 30.5	✓ Ro5	✓ Clean	`COc1cc2c(cc1OC)[C@H](CCc1ccccc1)NCC2`
ZINC2017274 ZINC	0.630	345.4 Da LogP 2.55 TPSA 80.2	✓ Ro5	Alert	`COc1cc(C[C@H]2NCCc3cc(O)c(O)cc32)cc(OC)c1OC`

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.