KpATCC43816 Protein target profile

phosphoenolpyruvate carboxykinase

Accession: VK055_3698

Gene: AIK82253.1 pckA2 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GWS6

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Length 540

Pocket druggability (P2Rank · AlphaFold DB model) 0.921

Metabolic reactions 1

Chokepoint No

Direct ligand evidence 0 16 total records

Functional annotation 1 EC 7 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

Central metabolic position More central than 99.7% 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. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.92. 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: 25.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 47.736 Higher values support similarity to known essential genes.
DEG E-value: 1.5900000000000002e-163 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 95.33 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) 0.921

Structure A0A0H3GWS6

Pocket Pocket 1

Druggability (FPocket) 0.267

Structure A0A0H3GWS6

Pocket Pocket 12

ColabFold model

P2Rank 0.93 · Pocket 1

FPocket 0.315 · Pocket 13

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 1198 / 4744 genomes with a hit

Prevalence 25.3%

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 99.7% of genes in this genome, no human homolog detected.

Relative network centrality 99.7% more central than 99.7% of genes in this genome

Chokepoint Not a chokepoint

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MRVNHGLTPQDLKAYGINDVQDIVHNPSYDMLFQEELDPNLEGYERGVLTTLGAIAVDTGIFTGRSPKDKYLVRDDTTRDTVWWSDKGKGKNDNKPLSQETWQHLKGLVTQQLSGKRLFIVDAFCGANADTRLSVRFITEVAWQAHFVKNMFIRPSDEELAEFVPDFIVMNGAKCTNPQWKEQGLNSENFVAFNLTERIQLIGGTWYGGEMKKGMFSIMNYLLPLKGIASMHCSANVGEKGDVAIFFGLSGTGKTTLSTDPKRRLIGDDEHGWDDDGVFNFEGGCYAKTIKLSEAAEPDIYHAIRRNALLENVVVRADGTVDFDDGSKTENTRVSYPIDHIDNIVKPVSKAGHATKVIFLTADAFGVLPPVSRLTADQTQYHFLSGFTAKLAGTERGVTEPTPTFSACFGAAFLSLHPTQYAEVLVKRMQAAGAQAYLVNTGWNGTGKRISIKDTRAIIDAILNGSLDNAETFTLPMFNLQIPTALPGVDTHILDPRSTYGSPEQWQEKADQLAKLFIENFEKYTDTPAGAALVAAGPQR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization: Cytoplasmic

Enzyme Commission (EC)

4.1.1.49

Gene Ontology (GO)

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0004612 Catalysis of the reaction: ATP + oxaloacetate = ADP + CO2 + H+ + phosphoenolpyruvate.
GO:0017076 Binding to a purine nucleotide, a compound consisting of a purine nucleoside esterified with (ortho)phosphate.
GO:0006094 The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
GO:0004611 Catalysis of the reaction: phosphate + oxaloacetate = phosphoenolpyruvate + CO2 + other reaction products.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

24 records

Show feature table

Start	End	DB	Term	Name
23	537	InterPro	IPR001272	Phosphoenolpyruvate carboxykinase, ATP-utilising
231	528	Gene3D	G3DSA:3.90.228.20	-
231	528	InterPro	IPR013035	Phosphoenolpyruvate carboxykinase, C-terminal
271	347	FunFam	G3DSA:2.170.8.10:FF:000001	Phosphoenolpyruvate carboxykinase (ATP)
23	537	CDD	cd00484	PEPCK_ATP
265	280	ProSitePatterns	PS00532	Phosphoenolpyruvate carboxykinase (ATP) signature.
265	280	InterPro	IPR015994	Phosphoenolpyruvate carboxykinase (ATP), conserved site
16	538	Hamap	MF_00453	Phosphoenolpyruvate carboxykinase (ATP) [pckA].
16	538	InterPro	IPR001272	Phosphoenolpyruvate carboxykinase, ATP-utilising
55	230	FunFam	G3DSA:3.40.449.10:FF:000001	Phosphoenolpyruvate carboxykinase (ATP)
9	227	SUPERFAMILY	SSF68923	PEP carboxykinase N-terminal domain
9	227	InterPro	IPR008210	Phosphoenolpyruvate carboxykinase, N-terminal
4	539	NCBIfam	TIGR00224	phosphoenolpyruvate carboxykinase (ATP)
4	539	InterPro	IPR001272	Phosphoenolpyruvate carboxykinase, ATP-utilising
229	539	SUPERFAMILY	SSF53795	PEP carboxykinase-like
3	540	PIRSF	PIRSF006294	PEP_crbxkin
3	540	InterPro	IPR001272	Phosphoenolpyruvate carboxykinase, ATP-utilising
15	230	Gene3D	G3DSA:3.40.449.10	Phosphoenolpyruvate Carboxykinase, domain 1
15	230	InterPro	IPR008210	Phosphoenolpyruvate carboxykinase, N-terminal
19	539	PANTHER	PTHR30031	PHOSPHOENOLPYRUVATE CARBOXYKINASE ATP
19	539	InterPro	IPR001272	Phosphoenolpyruvate carboxykinase, ATP-utilising
22	491	Pfam	PF01293	Phosphoenolpyruvate carboxykinase
22	491	InterPro	IPR001272	Phosphoenolpyruvate carboxykinase, ATP-utilising
43	346	Gene3D	G3DSA:2.170.8.10	Phosphoenolpyruvate Carboxykinase, domain 2

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

0.921

Likely same site as FPocket 1 4.0 Å 27 shared residues 93% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.046

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Surrounding area

Pocket 3 P2Rank #3

0.033

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Surrounding area

Pocket 4 P2Rank #4

0.023

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Surrounding area

Pocket 5 P2Rank #5

0.012

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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 #12

0.267

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Surrounding area

Pocket 2 FPocket #1

0.257

Likely same site as P2Rank 1 4.0 Å 27 shared residues 93% of smaller site

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Surrounding area

Residue sets

UniProt: Binding site:207-207

UniProt: Binding site:213-213

UniProt: Binding site:232-232

UniProt: Binding site:248-256

UniProt: Binding site:269-269

UniProt: Binding site:297-297

UniProt: Binding site:333-333

UniProt: Binding site:449-450

UniProt: Binding site:455-455

UniProt: Binding site:65-65

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

0.066

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Surrounding area

Pocket 3 P2Rank #3

0.042

Likely same site as FPocket 13 3.7 Å 8 shared residues 100% of smaller site

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Surrounding area

Pocket 4 P2Rank #4

0.024

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Surrounding area

Pocket 5 P2Rank #5

0.017

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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

0.315

Likely same site as P2Rank 3 3.7 Å 8 shared residues 100% of smaller site

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Surrounding area

Pocket 2 FPocket #23

0.276

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Surrounding area

Residue sets

UniProt: Binding site:207-207

UniProt: Binding site:213-213

UniProt: Binding site:232-232

UniProt: Binding site:248-256

UniProt: Binding site:269-269

UniProt: Binding site:297-297

UniProt: Binding site:333-333

UniProt: Binding site:449-450

UniProt: Binding site:455-455

UniProt: Binding site:65-65

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_A0A0H3GWS6	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_3698	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.

16 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 10 records from similar proteins

Structural ligands 10 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 6 similarity-based ZINC candidates

Best available ligand signal

03S PDB via homolog 96.1 Da · LogP -0.50 · TPSA 54.4 Open detail RCSB PDB

AF3 PDB via homolog Detail RCSB PDB

BTB PDB via homolog Detail RCSB PDB

CO2 PDB via homolog Detail RCSB PDB

DT3 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
03S RCSB PDB	6ASI	P22259	96.1 Da LogP -0.50 TPSA 54.4	✓ Ro5	✓ Clean	`CS(=O)(=O)O`
AF3 RCSB PDB	1K3C	P22259	84.0 Da LogP 0.88 TPSA 0.0	✓ Ro5	✓ Clean	`F[Al](F)F`
BTB RCSB PDB	6ASM	P22259	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`C(CO)N(CCO)C(CO)(CO)CO`
CO2 RCSB PDB	2OLR	P22259	44.0 Da LogP -0.58 TPSA 34.1	✓ Ro5	✓ Clean	`C(=O)=O`
DT3 RCSB PDB	1YLH	A6VKV4	201.2 Da LogP -1.82 TPSA 97.7	✓ Ro5	✓ Clean	`C([C@H]([C@@H](CS(=O)(=O)[O-])O)O)S`
OAA RCSB PDB	2PXZ	P22259	131.1 Da LogP -2.22 TPSA 94.5	✓ Ro5	✓ Clean	`C(C(=O)C(=O)O)C(=O)[O-]`
OXD RCSB PDB	1YTM	O09460	90.0 Da LogP -0.84 TPSA 74.6	✓ Ro5	✓ Clean	`C(=O)(C(=O)O)O`
OXL RCSB PDB	1AYL	P22259	88.0 Da LogP -3.51 TPSA 80.3	✓ Ro5	✓ Clean	`C(=O)(C(=O)[O-])[O-]`
PYR RCSB PDB	1AQ2	P22259	88.1 Da LogP -0.34 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)C(=O)O`
THJ RCSB PDB	6ASM	P22259	112.1 Da LogP -1.01 TPSA 57.2	✓ Ro5	✓ Clean	`[O-]S(=O)(=O)[S-]`

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
ZINC1615342 ZINC	1.000	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`OCCN(CCO)C(CO)(CO)CO`
ZINC2334905 ZINC	0.522	261.4 Da LogP 1.10 TPSA 63.9	✓ Ro5	✓ Clean	`CC(C)CCN(CCC(C)C)C(CO)(CO)CO`
ZINC3159953 ZINC	0.522	261.4 Da LogP 1.38 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCN(CCCCC)C(CO)(CO)CO`
ZINC5297554 ZINC	0.500	289.5 Da LogP 2.16 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCCN(CCCCCC)C(CO)(CO)CO`
ZINC97941822 ZINC	0.500	317.5 Da LogP 2.94 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCCCN(CCCCCCC)C(CO)(CO)CO`
ZINC97942927 ZINC	0.500	373.6 Da LogP 4.51 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCCCCCN(CCCCCCCCC)C(CO)(CO)CO`

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 A0A0H3GWS6

Pathways

KEGG R00341 BioCyc PEPCARBOXYKIN-RXN