KpATCC43816 Protein target profile

triose-phosphate isomerase

Accession: VK055_3463

Gene: AIK82019.1 tpiA2 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3H4K9

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Length 249

Pocket druggability (P2Rank · AlphaFold DB model) 0.635

Metabolic reactions 1

Chokepoint No

Direct ligand evidence 0 20 total records

Functional annotation 1 EC 6 GO

Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.64, FPocket 0.77). Use the 3D pocket comparison to verify whether they identify the same site. Central metabolic position More central than 99.3% of genes in this genome. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.77. This is a computational pocket signal, not binding validation. 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: Hit
Human identity (%): 57.576 Lower values reduce human off-target concern.
Human E-value: 1.74e-06
Gut microbiome similarity: 5.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 73.029 Higher values support similarity to known essential genes.
DEG E-value: 1.24e-124 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 96.99 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) 0.635

Structure A0A0H3H4K9

Pocket Pocket 1

Druggability (FPocket) 0.766

Structure A0A0H3H4K9

Pocket Pocket 7

ColabFold model

P2Rank 0.664 · Pocket 1

FPocket 0.642 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 239 / 4744 genomes with a hit

Prevalence 5.0%

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 99.3% of genes in this genome.

Relative network centrality 99.3% more central than 99.3% of genes in this genome

Chokepoint Not a chokepoint

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MGNWKLNGSRHMVNELVANLRTELAGVSGCAVAIAPPEMYLDLAKRAAEGSHIHLGAQNVDVNLSGAFTGETSAEMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGVVIAYEPVWAIGTGKSATPAQAQAVHKFIRDHIAKADAKIAEQVIIQYGGSVNAGNAAELFTQPDIDGALVGGASLKADAFAVIVKAAEAAKKA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization: Cytoplasmic

Enzyme Commission (EC)

5.3.1.1

Gene Ontology (GO)

GO:0006096 The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
GO:0004807 Catalysis of the reaction: D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0006094 The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
GO:0046166 The chemical reactions and pathways resulting in the formation of glyceraldehyde-3-phosphate, an important intermediate in glycolysis.
GO:0019563 The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
2	240	CDD	cd00311	TIM
2	240	InterPro	IPR000652	Triosephosphate isomerase
1	242	Pfam	PF00121	Triosephosphate isomerase
1	242	InterPro	IPR000652	Triosephosphate isomerase
1	247	FunFam	G3DSA:3.20.20.70:FF:000020	Triosephosphate isomerase
1	234	NCBIfam	TIGR00419	triose-phosphate isomerase
1	234	InterPro	IPR000652	Triosephosphate isomerase
2	241	PANTHER	PTHR21139	TRIOSEPHOSPHATE ISOMERASE
2	241	InterPro	IPR000652	Triosephosphate isomerase
2	242	SUPERFAMILY	SSF51351	Triosephosphate isomerase (TIM)
2	242	InterPro	IPR035990	Triosephosphate isomerase superfamily
1	242	Hamap	MF_00147_B	Triosephosphate isomerase [tpiA].
1	242	InterPro	IPR022896	Triosephosphate isomerase, bacterial/eukaryotic
159	169	ProSitePatterns	PS00171	Triosephosphate isomerase active site.
159	169	InterPro	IPR020861	Triosephosphate isomerase, active site
1	242	ProSiteProfiles	PS51440	Triosephosphate isomerase (TIM) family profile.
1	249	Gene3D	G3DSA:3.20.20.70	Aldolase class I
1	249	InterPro	IPR013785	Aldolase-type TIM barrel

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

0.635

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Surrounding area

Pocket 2 P2Rank #2

0.078

Likely same site as FPocket 2 1.1 Å 10 shared residues 91% of smaller site

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Surrounding area

Pocket 3 P2Rank #3

0.032

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Surrounding area

Pocket 4 P2Rank #4

0.027

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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 #7

0.766

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Surrounding area

Pocket 2 FPocket #2

0.56

Likely same site as P2Rank 2 1.1 Å 10 shared residues 91% of smaller site

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Surrounding area

Pocket 3 FPocket #1

0.508

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Surrounding area

Residue sets

UniProt: Active site:167-167 Proton acceptor

UniProt: Active site:95-95 Electrophile

UniProt: Binding site:173-173

UniProt: Binding site:212-212

UniProt: Binding site:233-234

UniProt: Binding site:9-11

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1

0.664

Likely same site as FPocket 1 1.2 Å 19 shared residues 95% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.649

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Surrounding area

Pocket 3 P2Rank #3

0.056

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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 #1

0.642

Likely same site as P2Rank 1 1.2 Å 19 shared residues 95% of smaller site

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Surrounding area

Pocket 2 FPocket #7

0.527

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Surrounding area

Residue sets

UniProt: Active site:167-167 Proton acceptor

UniProt: Active site:95-95 Electrophile

UniProt: Binding site:173-173

UniProt: Binding site:212-212

UniProt: Binding site:233-234

UniProt: Binding site:9-11

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_A0A0H3H4K9	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_3463	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.

20 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 3 records from similar proteins

Structural ligands 3 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 17 similarity-based ZINC candidates

Best available ligand signal

13P PDB via homolog 170.1 Da · LogP -1.34 · TPSA 104.1 Open detail RCSB PDB

PGA PDB via homolog Detail RCSB PDB

PGH PDB via homolog Detail RCSB PDB

ZINC1532902 ZINC proposed compound · Tanimoto 0.700 Detail ZINC

ZINC2018106 ZINC proposed compound · Tanimoto 0.700 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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
13P RCSB PDB	1NEY	P00942	170.1 Da LogP -1.34 TPSA 104.1	✓ Ro5	✓ Clean	`C(C(=O)COP(=O)(O)O)O`
PGA RCSB PDB	2YPI	P00942	156.0 Da LogP -0.82 TPSA 104.1	✓ Ro5	✓ Clean	`C(C(=O)O)OP(=O)(O)O`
PGH RCSB PDB	3YPI	P00942	171.0 Da LogP -1.40 TPSA 116.1	✓ Ro5	✓ Clean	`C(C(=O)NO)OP(=O)(O)O`

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 A0A0H3H4K9

Pathways

KEGG R01015 BioCyc TRIOSEPISOMERIZATION-RXN