Protein target profile

KP13_02899

Acetoin:2,6-dichlorophenolindophenol oxidoreductase subunit beta

Genome: KpKP13 Gene: acoB AHE46175.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GIT5

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Length 342

Pocket druggability 0.823

Direct ligand evidence 0 21 total records

Functional annotation 0 EC 2 GO

Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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

Main supporting evidence

Strong predicted binding pocket FPocket selected-pocket score 0.82. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 8 structural and 0 bioactivity records.

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: Hit
Human identity (%): 40.0 Lower values reduce human off-target concern.
Human E-value: 2.9700000000000003e-47
Gut microbiome similarity: 1.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 45.614 Higher values support similarity to known essential genes.
DEG E-value: 4.6499999999999995e-95 Smaller values mean stronger essential-gene similarity.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 95.29 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 0.823

Structure A0A0H3GIT5

Pocket Pocket 3

P2Rank 0.06

Structure A0A0H3GIT5

Pocket Pocket 1

ColabFold model

FPocket 0.886 · Pocket 3

P2Rank 0.077 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 60 / 4744 genomes with a hit

Prevalence 1.3%

Cross-references

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

Sequence

UniProt A0A0H3GIT5

Sequence

Primary amino-acid sequence viewer.

MITMTIKTYREAVKEALAQEMERDERVVLIGEDLRGGHGGNAPEEAKIEAFGGVLGVTKGLWTQFGSDRVIDTPITESAIIGMAAGAAATGLRPVAELMFMDFFGVSHDALYNQAAKFRYMFGGKARAPLVMRGMIGAGFSAAAQHSQSPYNIFATTPGLKVVVPSTPYDVKGLLIQSIRDDDPVVFCEHKMLYDLKGEVPDEIYTIPLGVANYTREGEDVTIIALSAMVHKANQVADKLAREGISVEVVDPRTISPLDEEGILESVASTGRVVIVDESAARFGFAHDVAALIASQAFHFLKAPVLLVTPPHTPVPFSPALEKLWIPGVERIEAAVRQVLED

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
4	208	FunFam	G3DSA:3.40.50.970:FF:000001	Pyruvate dehydrogenase E1 beta subunit
209	341	FunFam	G3DSA:3.40.50.920:FF:000001	Pyruvate dehydrogenase E1 beta subunit
4	210	Gene3D	G3DSA:3.40.50.970	-
4	340	PANTHER	PTHR43257	PYRUVATE DEHYDROGENASE E1 COMPONENT BETA SUBUNIT
210	332	Pfam	PF02780	Transketolase, C-terminal domain
210	332	InterPro	IPR033248	Transketolase, C-terminal domain
7	196	SMART	SM00861	Transket_pyr_3
7	196	InterPro	IPR005475	Transketolase-like, pyrimidine-binding domain
4	220	SUPERFAMILY	SSF52518	Thiamin diphosphate-binding fold (THDP-binding)
4	220	InterPro	IPR029061	Thiamin diphosphate-binding fold
8	195	Pfam	PF02779	Transketolase, pyrimidine binding domain
8	195	InterPro	IPR005475	Transketolase-like, pyrimidine-binding domain
329	342	Coils	Coil	Coil
11	191	CDD	cd07036	TPP_PYR_E1-PDHc-beta_like
211	341	Gene3D	G3DSA:3.40.50.920	-
211	341	InterPro	IPR009014	Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II
205	340	SUPERFAMILY	SSF52922	TK C-terminal domain-like
205	340	InterPro	IPR009014	Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II

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 #3

0.823

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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

0.06

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Surrounding area

Site 2 P2Rank #2

0.06

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Surrounding area

Site 3 P2Rank #3

0.035

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Surrounding area

Site 4 P2Rank #4

0.018

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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

0.077

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Surrounding area

Site 2 P2Rank #2

0.063

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Surrounding area

Site 3 P2Rank #3

0.047

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Surrounding area

Site 4 P2Rank #4

0.023

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Surrounding area

Site 5 P2Rank #5

0.013

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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_A0A0H3GIT5	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_02899	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.

21 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 8 records from similar proteins

Structural ligands 8 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 13 similarity-based ZINC candidates

Best available ligand signal

4MV PDB via homolog 116.2 Da · LogP 1.51 · TPSA 37.3 Open detail RCSB PDB

A5X PDB via homolog Detail RCSB PDB

COI PDB via homolog Detail RCSB PDB

PYR PDB via homolog Detail RCSB PDB

THV 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
4MV RCSB PDB	1UMC	Q5SLR3	116.2 Da LogP 1.51 TPSA 37.3	✓ Ro5	✓ Clean	`CC(C)CCC(=O)O`
A5X RCSB PDB	6CFO	P11177	533.4 Da LogP 0.47 TPSA 226.5	2 viol.	✓ Clean	`Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](C)(O)P(=O)O)CC…`
COI RCSB PDB	1QS0	P09061	130.1 Da LogP 0.69 TPSA 54.4	✓ Ro5	✓ Clean	`CC(C)CC(=O)C(=O)O`
PYR RCSB PDB	3DV0	P21874	88.1 Da LogP -0.34 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)C(=O)O`
THV RCSB PDB	2BEU	P21953	496.4 Da LogP 1.75 TPSA 189.2	✓ Ro5	✓ Clean	`Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C-](C(C)C)O)CCO[P@@…`
THW RCSB PDB	2BEW	P21953	530.4 Da LogP 2.14 TPSA 189.2	1 viol.	✓ Clean	`Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C-](c3ccccc3)O)CCO[…`
THY RCSB PDB	2BEV	P21953	510.4 Da LogP 2.14 TPSA 189.2	1 viol.	✓ Clean	`CC[C@H](C)[C-](c1[n+](c(c(s1)CCO[P@](=O)(O)OP(=…`
TZD RCSB PDB	2BFC	P21953	440.3 Da LogP 0.72 TPSA 187.1	✓ Ro5	✓ Clean	`Cc1ncc(c(n1)N)CN2C(=C(SC2=O)CCO[P@@](=O)(O)OP(=…`

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
ZINC1841074 ZINC	0.636	200.3 Da LogP 3.85 TPSA 37.3	✓ Ro5	✓ Clean	`CC(C)CCCCCCCCC(=O)O`
ZINC2013445 ZINC	0.636	214.3 Da LogP 4.24 TPSA 37.3	✓ Ro5	✓ Clean	`CC(C)CCCCCCCCCC(=O)O`
ZINC2575042 ZINC	0.636	228.4 Da LogP 4.63 TPSA 37.3	✓ Ro5	✓ Clean	`CC(C)CCCCCCCCCCC(=O)O`
ZINC8215517 ZINC	0.618	425.3 Da LogP 0.84 TPSA 169.0	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCO[P@@](=O)(O)OP(=O)(O)O)c2C)…`
ZINC145838685 ZINC	0.583	200.3 Da LogP 3.70 TPSA 37.3	✓ Ro5	✓ Clean	`CC(C)CCC[C@@H](C)CCCC(=O)O`
ZINC145838882 ZINC	0.583	200.3 Da LogP 3.70 TPSA 37.3	✓ Ro5	✓ Clean	`CC(C)CCC[C@H](C)CCCC(=O)O`
ZINC13540298 ZINC	0.556	440.3 Da LogP 0.72 TPSA 187.1	✓ Ro5	✓ Clean	`Cc1ncc(Cn2c(C)c(CCO[P@@](=O)(O)OP(=O)(O)O)sc2=O…`
ZINC2492519 ZINC	0.542	201.3 Da LogP 2.08 TPSA 40.5	✓ Ro5	✓ Clean	`CC(C)CN(CCC(=O)O)CC(C)C`
ZINC1532839 ZINC	0.529	345.3 Da LogP 0.72 TPSA 122.4	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOP(=O)(O)O)c2C)c(N)n1`
ZINC13520374 ZINC	0.528	426.3 Da LogP 0.97 TPSA 163.2	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCO[P@@](=O)(O)OP(=O)(O)O)c2C)…`
ZINC1690029 ZINC	0.524	204.2 Da LogP 0.42 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)CCC(CCC(=O)O)C(=O)O`
ZINC96509633 ZINC	0.522	228.2 Da LogP 1.89 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCC(CCC(=O)O)C(F)(F)F`
ZINC4784097 ZINC	0.500	201.3 Da LogP 1.40 TPSA 66.4	✓ Ro5	✓ Clean	`CC(C)CCNC(=O)CCCC(=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.