KpATCC43816 Protein target profile

citrate lyase, alpha subunit

Accession: VK055_2538

Gene: citF AIK81135.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GI24

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Length 508

Pocket druggability (P2Rank · AlphaFold DB model) 0.93

Metabolic reactions 2

Chokepoint Yes

Direct ligand evidence 0 17 total records

Functional annotation 2 EC 5 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

Metabolic chokepoint Catalyzes a reaction that is the only producer or consumer of a metabolite in the imported metabolic model. Central metabolic position More central than 95.1% of genes in this genome. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Second pocket predictor agrees P2Rank predicted binding-site probability 0.93. Review the complete evidence below

Risks to review

Evidence coverage

Core evidence streams are available for this target.

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: 7.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 72.068 Higher values support similarity to known essential genes.
DEG E-value: 0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 97.15 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) 0.93

Structure A0A0H3GI24

Pocket Pocket 1

Druggability (FPocket) 0.248

Structure A0A0H3GI24

Pocket Pocket 2

ColabFold model

P2Rank 0.92 · Pocket 1

FPocket 0.26 · Pocket 3

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 340 / 4744 genomes with a hit

Prevalence 7.2%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Attractive metabolic target: catalyzes a producing chokepoint reaction, more central than 95.1% of genes in this genome, no human homolog detected.

Relative network centrality 95.1% more central than 95.1% of genes in this genome

Chokepoint Chokepoint gene

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MKETVAMLNQQYVMPNGLTPYAGVTAKSPWLASESEKRQRKICDSLETAIRRSGLQNGMTISFHHAFRGGDKVVNMVVAKLAEMGFRDLTLASSSLIDAHWPLIEHIKNGVIRQIYTSGLRGKLGEEISAGLMENPVQIHSHGGRVQLIQSGELSIDVAFLGVPCCDEFGNANGFSGKSRCGSLGYARVDAEHAKCVVLLTEEWVDYPNYPASIAQDQVDLIVQVDEVGDPQKITAGAIRLTSNPRELLIARQAAKVVEHSGYFKEGFSLQTGTGGASLAVTRFLEDKMRRNGITASFGLGGITGTMVDLHEKGLIKTLLDTQSFDGDAARSLAQNPNHVEISTNQYASPGSKGASCERLNVVMLSALEIDIDFNVNVMTGSNGVLRGASGGHSDTAAGADLTIITAPLVRGRIPCVVEKVLTRVTPGASVDVLVTDHGIAVNPARQDLIDNLRSAGIPLMTIEELQQRAELLTGKPQPIEFTDRVVAVVRYRDGSVIDVIRQVKNSD

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 5 GO

Subcellular localization

Localization: Cytoplasmic

Enzyme Commission (EC)

Gene Ontology (GO)

GO:0006084 The chemical reactions and pathways involving acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated; it is a metabolite derived from several pathways (e.g. glycolysis, fatty acid oxidation, amino-acid catabolism) and is further metabolized by the tricarboxylic acid cycle. It is a key intermediate in lipid and terpenoid biosynthesis.
GO:0008814 Catalysis of the reaction: acetyl-CoA + citrate = acetate + (3S)-citryl-CoA.
GO:0009346 Citrate lyase is a multienzyme complex with three constituents: the alpha subunit, citrate-ACP transferase; the beta subunit, citryl-ACP lyase; and the gamma subunit, an acyl-carrier protein which also carries the prosthetic group components. All three subunits are required for citrate lyase enzyme activity. This enzyme has only been found in bacteria.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0008815 Catalysis of the reaction: citrate = acetate + oxaloacetate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

13 records

Show feature table

Start	End	DB	Term	Name
36	506	NCBIfam	TIGR01584	citrate lyase subunit alpha
36	506	InterPro	IPR006472	Citrate lyase, alpha subunit
1	506	PIRSF	PIRSF009451	Citrt_lyas_alpha
1	506	InterPro	IPR006472	Citrate lyase, alpha subunit
7	234	SUPERFAMILY	SSF100950	NagB/RpiA/CoA transferase-like
7	234	InterPro	IPR037171	NagB/RpiA transferase-like
238	504	SUPERFAMILY	SSF100950	NagB/RpiA/CoA transferase-like
238	504	InterPro	IPR037171	NagB/RpiA transferase-like
1	235	Gene3D	G3DSA:3.40.1080.10	-
237	506	Gene3D	G3DSA:3.40.1080.10	-
40	504	Pfam	PF04223	Citrate lyase, alpha subunit (CitF)
40	504	InterPro	IPR006472	Citrate lyase, alpha subunit
1	506	PANTHER	PTHR40596	CITRATE LYASE ALPHA CHAIN

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

0.93

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Surrounding area

Pocket 2 P2Rank #2

0.095

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Surrounding area

Pocket 3 P2Rank #3

0.018

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Surrounding area

Pocket 4 P2Rank #4

0.005

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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 #2

0.248

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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_A0A0H3GI24	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_2538	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.

17 records

Chemistry signal

Only proposed virtual-screening candidates are available for this target.

Direct evidence 0 same-protein records

Transferred evidence 0 records from similar proteins

Structural ligands 0 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 17 similarity-based ZINC candidates

Best available ligand signal

ZINC1532902 ZINC proposed compound Tanimoto 0.700 206.2 Da · LogP -0.86 · TPSA 132.1 Open detail ZINC

ZINC2018106 ZINC proposed compound · Tanimoto 0.700 Detail ZINC

ZINC3593496 ZINC proposed compound · Tanimoto 0.652 Detail ZINC

ZINC3593497 ZINC proposed compound · Tanimoto 0.652 Detail ZINC

ZINC14686440 ZINC proposed compound · Tanimoto 0.625 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.

No PDB ligands found through similar proteins.

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
ZINC1532902 ZINC	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106 ZINC	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC3593496 ZINC	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497 ZINC	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC14686440 ZINC	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442 ZINC	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444 ZINC	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC13398039 ZINC	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC2528012 ZINC	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC146315135 ZINC	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@@](O)(CC(=O)O)C(=O)O`
ZINC146315336 ZINC	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@](O)(CC(=O)O)C(=O)O`
ZINC1850353 ZINC	0.556	206.1 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC(O)(CC(=O)O)CC(=O)O`
ZINC13398014 ZINC	0.522	220.2 Da LogP -1.07 TPSA 110.1	✓ Ro5	✓ Clean	`COC(=O)CC(O)(CC(=O)OC)C(=O)O`
ZINC3861629 ZINC	0.522	206.1 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C(O)(CC(=O)O)CC(=O)O`
ZINC100969993 ZINC	0.500	359.5 Da LogP 2.70 TPSA 123.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC100969996 ZINC	0.500	359.5 Da LogP 2.70 TPSA 123.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC1711854 ZINC	0.500	248.2 Da LogP -0.13 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)CC(CC(=O)O)(CC(=O)O)CC(=O)O`

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 A0A0H3GI24

Pathways

KEGG R01323 BioCyc 2.8.3.10-RXN BioCyc CITTRANS-RXN