KpATCC43816 Protein target profile

3-oxoadipate CoA-transferase subunit A

Accession: VK055_0965

Gene: AIK79588.1 pcaI 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GWW0

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Length 228

Pocket druggability (P2Rank · AlphaFold DB model) 0.013

Metabolic reactions 2

Chokepoint Yes

Direct ligand evidence 0 54 total records

Functional annotation 0 EC 1 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 98.4% of genes in this genome. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Human similarity Top human hit identity: 48.235%. Microbiome similarity 76 of 4744 screened genomes (1.6%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.18. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.01.

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 (%): 48.235 Lower values reduce human off-target concern.
Human E-value: 4.34e-21
Gut microbiome similarity: 1.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 75.882 Higher values support similarity to known essential genes.
DEG E-value: 1.66e-94 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 96.93 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) 0.013

Structure A0A0H3GWW0

Pocket Pocket 1

Druggability (FPocket) 0.178

Structure A0A0H3GWW0

Pocket Pocket 6

ColabFold model

P2Rank 0.045 · Pocket 1

FPocket 0.365 · Pocket 5

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 76 / 4744 genomes with a hit

Prevalence 1.6%

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a consuming chokepoint reaction in Benzoate degradation, more central than 98.4% of genes in this genome.

Relative network centrality 98.4% more central than 98.4% of genes in this genome

Chokepoint Chokepoint gene

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MIDKSVSTLSEAIAGIHDGATIMIGGFGPAGQPTFLIDALIDQGARDLTIINNNAGNGEVGLAALLKAGRVRKMICSFPRQVDSQIFDDLYRRGKVELELVPQGNLAARIQAAGAGLGAVFTPTGYGTPLAEGKETREIDGRHYVLEYPIKADFALIKAHQGDRWGNLVYRKAARNFGPIMATAAKTTIVEVSQLVALGDLDPENIITPGIFVQRVFSLENLTAAQRA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

GO:0008410 Catalysis of the transfer of a coenzyme A (CoA) group from one compound (donor) to another (acceptor).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

13 records

Show feature table

Start	End	DB	Term	Name
6	219	SMART	SM00882	CoA_trans_3
6	219	InterPro	IPR004165	Coenzyme A transferase family I
7	217	Pfam	PF01144	Coenzyme A transferase
7	217	InterPro	IPR004165	Coenzyme A transferase family I
18	33	ProSitePatterns	PS01273	Coenzyme A transferases signature 1.
18	33	InterPro	IPR004163	Coenzyme A transferase binding site
1	220	NCBIfam	TIGR02429	3-oxoacid CoA-transferase subunit A
1	220	InterPro	IPR012792	3-oxoacid CoA-transferase, subunit A
4	221	PANTHER	PTHR13707	KETOACID-COENZYME A TRANSFERASE
4	221	InterPro	IPR004165	Coenzyme A transferase family I
2	221	SUPERFAMILY	SSF100950	NagB/RpiA/CoA transferase-like
2	221	InterPro	IPR037171	NagB/RpiA transferase-like
1	224	Gene3D	G3DSA:3.40.1080.10	-

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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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

0.013

Show in viewer

Surrounding area

Pocket 2 P2Rank #2

0.002

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_A0A0H3GWW0	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_0965	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.

54 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 4 records from similar proteins

Structural ligands 4 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

4PS PDB via homolog 438.3 Da · LogP -0.85 · TPSA 191.7 Open detail RCSB PDB

8EW PDB via homolog Detail RCSB PDB

8EZ PDB via homolog Detail RCSB PDB

F8G PDB via homolog Detail RCSB PDB

ZINC393371 ZINC proposed compound · Tanimoto 0.650 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
4PS RCSB PDB	5MZX	Q1D4I4	438.3 Da LogP -0.85 TPSA 191.7	1 viol.	✓ Clean	`CC(C)(CO[P@](=O)(O)OP(=O)(O)O)[C@H](C(=O)NCCC(=…`
8EW RCSB PDB	5MZZ	Q1D4I4	144.1 Da LogP 0.49 TPSA 74.6	✓ Ro5	✓ Clean	`CC(=CC(=O)O)CC(=O)O`
8EZ RCSB PDB	5MZY	Q1D4I4	142.2 Da LogP 1.90 TPSA 37.3	✓ Ro5	✓ Clean	`C[C@H]1CCCC[C@H]1C(=O)O`
F8G RCSB PDB	6CO9	Q0S7P9	975.8 Da LogP -0.02 TPSA 410.2	3 viol.	✓ Clean	`C[C@@H]1CCC(=C([C@@]12CCC(=O)O2)C(=O)SCCNC(=O)C…`

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
ZINC393371 ZINC	0.650	200.2 Da LogP 1.74 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)[C@H]1CCCCCC[C@H]1C(=O)O`
ZINC4569505 ZINC	0.650	200.2 Da LogP 1.74 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)[C@@H]1CCCCCC[C@H]1C(=O)O`
ZINC4569508 ZINC	0.650	200.2 Da LogP 1.74 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)[C@H]1CCCCCC[C@@H]1C(=O)O`
ZINC3869683 ZINC	0.587	278.4 Da LogP -1.08 TPSA 98.7	✓ Ro5	✓ Clean	`CC(C)(CO)[C@H](O)C(=O)NCCC(=O)NCCS`
ZINC3869684 ZINC	0.587	278.4 Da LogP -1.08 TPSA 98.7	✓ Ro5	✓ Clean	`CC(C)(CO)[C@@H](O)C(=O)NCCC(=O)NCCS`
ZINC1857784586 ZINC	0.577	204.2 Da LogP 2.25 TPSA 54.4	✓ Ro5	✓ Clean	`CP(C)(=O)[C@@H]1CCCC[C@H]1C(=O)O`
ZINC1857784587 ZINC	0.577	204.2 Da LogP 2.25 TPSA 54.4	✓ Ro5	✓ Clean	`CP(C)(=O)[C@@H]1CCCC[C@@H]1C(=O)O`
ZINC1857784588 ZINC	0.577	204.2 Da LogP 2.25 TPSA 54.4	✓ Ro5	✓ Clean	`CP(C)(=O)[C@H]1CCCC[C@H]1C(=O)O`
ZINC1857784589 ZINC	0.577	204.2 Da LogP 2.25 TPSA 54.4	✓ Ro5	✓ Clean	`CP(C)(=O)[C@H]1CCCC[C@@H]1C(=O)O`
ZINC239222057 ZINC	0.552	267.4 Da LogP 2.57 TPSA 66.4	✓ Ro5	✓ Clean	`C[C@@H]1CCCC[C@@H]1NC(=O)[C@@H]1CCCC[C@H]1C(=O)O`
ZINC239222058 ZINC	0.552	267.4 Da LogP 2.57 TPSA 66.4	✓ Ro5	✓ Clean	`C[C@@H]1CCCC[C@@H]1NC(=O)[C@H]1CCCC[C@@H]1C(=O)O`
ZINC239222059 ZINC	0.552	267.4 Da LogP 2.57 TPSA 66.4	✓ Ro5	✓ Clean	`C[C@@H]1CCCC[C@@H]1NC(=O)[C@H]1CCCC[C@H]1C(=O)O`
ZINC4614604 ZINC	0.552	267.4 Da LogP 2.57 TPSA 66.4	✓ Ro5	✓ Clean	`C[C@@H]1CCCC[C@@H]1NC(=O)[C@@H]1CCCC[C@@H]1C(=O…`
ZINC4614605 ZINC	0.552	267.4 Da LogP 2.57 TPSA 66.4	✓ Ro5	✓ Clean	`C[C@H]1CCCC[C@@H]1NC(=O)[C@@H]1CCCC[C@@H]1C(=O)O`
ZINC4614606 ZINC	0.552	267.4 Da LogP 2.57 TPSA 66.4	✓ Ro5	✓ Clean	`C[C@@H]1CCCC[C@H]1NC(=O)[C@@H]1CCCC[C@@H]1C(=O)O`
ZINC4614607 ZINC	0.552	267.4 Da LogP 2.57 TPSA 66.4	✓ Ro5	✓ Clean	`C[C@H]1CCCC[C@H]1NC(=O)[C@@H]1CCCC[C@@H]1C(=O)O`
ZINC12649639 ZINC	0.536	228.3 Da LogP 2.22 TPSA 63.6	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)[C@@H]1CCCC[C@@H]1C(=O)O`
ZINC12649643 ZINC	0.536	228.3 Da LogP 2.22 TPSA 63.6	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)[C@H]1CCCC[C@@H]1C(=O)O`
ZINC12649649 ZINC	0.536	228.3 Da LogP 2.22 TPSA 63.6	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)[C@@H]1CCCC[C@H]1C(=O)O`
ZINC12649652 ZINC	0.536	228.3 Da LogP 2.22 TPSA 63.6	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)[C@H]1CCCC[C@H]1C(=O)O`
ZINC225460408 ZINC	0.536	212.2 Da LogP 2.07 TPSA 74.6	✓ Ro5	✓ Clean	`C/C(=C\C(=O)O)C/C(C)=C/[C@H](C)C(=O)O`
ZINC225460436 ZINC	0.536	212.2 Da LogP 2.07 TPSA 74.6	✓ Ro5	✓ Clean	`C/C(=C\C(=O)O)C/C(C)=C/[C@@H](C)C(=O)O`
ZINC60138437 ZINC	0.522	226.3 Da LogP 1.99 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)[C@H]1CC[C@@H](C(=O)O)[C@@H]2CCCC[C@@H]12`
ZINC60138439 ZINC	0.522	226.3 Da LogP 1.99 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)[C@H]1CC[C@@H](C(=O)O)[C@@H]2CCCC[C@H]12`
ZINC60138442 ZINC	0.522	226.3 Da LogP 1.99 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)[C@H]1CC[C@@H](C(=O)O)[C@H]2CCCC[C@@H]12`
ZINC60138444 ZINC	0.522	226.3 Da LogP 1.99 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)[C@H]1CC[C@@H](C(=O)O)[C@H]2CCCC[C@H]12`
ZINC514278434 ZINC	0.520	283.5 Da LogP 4.49 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H]1CCCCCCCCCCCCCC[C@H]1C(=O)O`
ZINC257836113 ZINC	0.519	206.3 Da LogP 0.67 TPSA 71.4	✓ Ro5	✓ Clean	`CS(=O)(=O)[C@H]1CCCC[C@@H]1C(=O)O`
ZINC257836114 ZINC	0.519	206.3 Da LogP 0.67 TPSA 71.4	✓ Ro5	✓ Clean	`CS(=O)(=O)[C@@H]1CCCC[C@@H]1C(=O)O`
ZINC257836115 ZINC	0.519	206.3 Da LogP 0.67 TPSA 71.4	✓ Ro5	✓ Clean	`CS(=O)(=O)[C@@H]1CCCC[C@H]1C(=O)O`
ZINC257836116 ZINC	0.519	206.3 Da LogP 0.67 TPSA 71.4	✓ Ro5	✓ Clean	`CS(=O)(=O)[C@H]1CCCC[C@H]1C(=O)O`
ZINC12291864 ZINC	0.517	267.4 Da LogP 2.67 TPSA 57.6	✓ Ro5	✓ Clean	`CN(C(=O)[C@@H]1CCCC[C@@H]1C(=O)O)C1CCCCC1`
ZINC12291865 ZINC	0.517	267.4 Da LogP 2.67 TPSA 57.6	✓ Ro5	✓ Clean	`CN(C(=O)[C@H]1CCCC[C@@H]1C(=O)O)C1CCCCC1`
ZINC12291866 ZINC	0.517	267.4 Da LogP 2.67 TPSA 57.6	✓ Ro5	✓ Clean	`CN(C(=O)[C@@H]1CCCC[C@H]1C(=O)O)C1CCCCC1`
ZINC12291869 ZINC	0.517	267.4 Da LogP 2.67 TPSA 57.6	✓ Ro5	✓ Clean	`CN(C(=O)[C@H]1CCCC[C@H]1C(=O)O)C1CCCCC1`
ZINC10109826 ZINC	0.500	241.3 Da LogP 2.04 TPSA 66.4	✓ Ro5	✓ Clean	`CC(C)[C@H](NC(=O)[C@H]1CCCC[C@H]1C)C(=O)O`
ZINC10109828 ZINC	0.500	241.3 Da LogP 2.04 TPSA 66.4	✓ Ro5	✓ Clean	`CC(C)[C@H](NC(=O)[C@@H]1CCCC[C@H]1C)C(=O)O`
ZINC10109829 ZINC	0.500	241.3 Da LogP 2.04 TPSA 66.4	✓ Ro5	✓ Clean	`CC(C)[C@H](NC(=O)[C@@H]1CCCC[C@@H]1C)C(=O)O`
ZINC129835 ZINC	0.500	213.3 Da LogP 1.40 TPSA 66.4	✓ Ro5	✓ Clean	`CC(C)NC(=O)[C@H]1CCCC[C@H]1C(=O)O`
ZINC129837 ZINC	0.500	213.3 Da LogP 1.40 TPSA 66.4	✓ Ro5	✓ Clean	`CC(C)NC(=O)[C@@H]1CCCC[C@H]1C(=O)O`
ZINC129838 ZINC	0.500	213.3 Da LogP 1.40 TPSA 66.4	✓ Ro5	✓ Clean	`CC(C)NC(=O)[C@H]1CCCC[C@@H]1C(=O)O`
ZINC129840 ZINC	0.500	213.3 Da LogP 1.40 TPSA 66.4	✓ Ro5	✓ Clean	`CC(C)NC(=O)[C@@H]1CCCC[C@@H]1C(=O)O`
ZINC200047 ZINC	0.500	255.4 Da LogP 2.52 TPSA 57.6	✓ Ro5	✓ Clean	`CC(C)N(C(=O)[C@H]1CCCC[C@H]1C(=O)O)C(C)C`
ZINC239377527 ZINC	0.500	281.4 Da LogP 2.82 TPSA 66.4	✓ Ro5	✓ Clean	`C[C@@H]1[C@@H](NC(=O)[C@@H]2CCCC[C@H]2C(=O)O)CC…`
ZINC239377528 ZINC	0.500	281.4 Da LogP 2.82 TPSA 66.4	✓ Ro5	✓ Clean	`C[C@@H]1CCC[C@H](NC(=O)[C@@H]2CCCC[C@H]2C(=O)O)…`
ZINC307303830 ZINC	0.500	211.3 Da LogP 1.73 TPSA 49.3	✓ Ro5	✓ Clean	`C[C@@H]1CCCC[C@@H]1[C@H]1CNC[C@H]1C(=O)O`
ZINC307303833 ZINC	0.500	211.3 Da LogP 1.73 TPSA 49.3	✓ Ro5	✓ Clean	`C[C@@H]1CCCC[C@@H]1[C@@H]1CNC[C@@H]1C(=O)O`
ZINC307303839 ZINC	0.500	211.3 Da LogP 1.73 TPSA 49.3	✓ Ro5	✓ Clean	`C[C@@H]1CCCC[C@@H]1[C@H]1CNC[C@@H]1C(=O)O`
ZINC4614682 ZINC	0.500	281.4 Da LogP 2.82 TPSA 66.4	✓ Ro5	✓ Clean	`C[C@@H]1CCC[C@H](NC(=O)[C@@H]2CCCC[C@@H]2C(=O)O…`
ZINC4614684 ZINC	0.500	281.4 Da LogP 2.82 TPSA 66.4	✓ Ro5	✓ Clean	`C[C@@H]1CCC[C@@H](NC(=O)[C@@H]2CCCC[C@@H]2C(=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 A0A0H3GWW0

Pathways

BioCyc RXN-10085 KEGG R02990 BioCyc 3-OXOADIPATE-COA-TRANSFERASE-RXN

3-oxoadipate CoA-transferase subunit A

Promising target candidate with multiple supporting evidence streams.

Main supporting evidence

Risks to review

Evidence coverage

Prioritization evidence

Off-target risk

Essentiality

Structure confidence

Binding-site evidence

Metabolic context

Sequence

Functional annotations

Subcellular localization

Gene Ontology (GO)

Sequence domains and features

3D structure

Binding pockets · P2Rank

Binding pockets · P2Rank

Binding pockets · FPocket

Structural evidence

Ligand evidence

Cross-references

Sequence

Pathways