KpATCC43816 Protein target profile

4-hydroxythreonine-4-phosphate dehydrogenase

Accession: VK055_1342

Gene: AIK79965.1 pdxA3 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A6T7I3

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Length 335

Pocket druggability (P2Rank · AlphaFold DB model) 0.748

Metabolic reactions 1

Chokepoint Yes

Direct ligand evidence 0 35 total records

Functional annotation 0 EC 1 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

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 88.2% 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. Moderate predicted binding pocket FPocket selected-pocket score 0.54. This supports review but is not experimental 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: No hit
Gut microbiome similarity: 0.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 37.615 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT: 96.7 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) 0.748

Structure A6T7I3

Pocket Pocket 1

Druggability (FPocket) 0.536

Structure A6T7I3

Pocket Pocket 2

ColabFold model

P2Rank 0.815 · Pocket 1

FPocket 0.769 · Pocket 4

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 33 / 4744 genomes with a hit

Prevalence 0.7%

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 88.2% of genes in this genome, no human homolog detected.

Relative network centrality 88.2% more central than 88.2% of genes in this genome

Chokepoint Chokepoint gene

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSAEKKPVVAITIGDPAGIGPEITVATMMDKSVYDECKPFLIGSVPIISRAMKIMGCDFAIHKIAHPQEARFSWGTLDVLETGDYDCDSIEWGKVQKLAGQMSLDYVMKSIELGKAGLIDVVSTAPIHKEAIKLAGCKLPGHTEIYQVETQSDYGLTMFHVHNLRVFFVSRHMALKAACDYANKARVLACVQQIHHEFTALNIKNPRIAVAALNPHGSDNGLFGHEEADNLIPAVKAAQEMGIKAIGPVPADSVFHLGKQGRYDAILSLYHDQGHIACKTLDFERSITITFGLPFMRSSVDHGTAFDIAGTGKAGTVSMLESTLVAARYWKMKHQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

GO:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

8 records

Show feature table

Start	End	DB	Term	Name
36	324	Pfam	PF04166	Pyridoxal phosphate biosynthetic protein PdxA
36	324	InterPro	IPR005255	PdxA family
9	328	NCBIfam	TIGR00557	4-hydroxythreonine-4-phosphate dehydrogenase PdxA
9	328	InterPro	IPR005255	PdxA family
5	333	PANTHER	PTHR30004	4-HYDROXYTHREONINE-4-PHOSPHATE DEHYDROGENASE
5	333	InterPro	IPR005255	PdxA family
1	332	Gene3D	G3DSA:3.40.718.10	Isopropylmalate Dehydrogenase
6	330	SUPERFAMILY	SSF53659	Isocitrate/Isopropylmalate dehydrogenase-like

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

0.748

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Surrounding area

Pocket 2 P2Rank #2

0.201

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Surrounding area

Pocket 3 P2Rank #3

0.121

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Surrounding area

Pocket 4 P2Rank #4

0.019

Likely same site as FPocket 2 2.9 Å 7 shared residues 100% of smaller site

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Surrounding area

Pocket 5 P2Rank #5

0.013

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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

0.536

Likely same site as P2Rank 4 2.9 Å 7 shared residues 100% of smaller site

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Surrounding area

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.815

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Surrounding area

Pocket 2 P2Rank #2

0.146

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Surrounding area

Pocket 3 P2Rank #3

0.088

Likely same site as FPocket 4 0.9 Å 8 shared residues 100% of smaller site

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Surrounding area

Pocket 4 P2Rank #4

0.057

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Surrounding area

Pocket 5 P2Rank #5

0.009

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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_A6T7I3	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_1342	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.

35 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 2 records from similar proteins

Structural ligands 2 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 33 similarity-based ZINC candidates

Best available ligand signal

4TP PDB via homolog 215.1 Da · LogP -2.13 · TPSA 150.3 Open detail RCSB PDB

POP PDB via homolog Detail RCSB PDB

ZINC12501558 ZINC proposed compound · Tanimoto 0.594 Detail ZINC

ZINC12501560 ZINC proposed compound · Tanimoto 0.594 Detail ZINC

ZINC12501562 ZINC proposed compound · Tanimoto 0.594 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
4TP RCSB PDB	1PS6	P19624	215.1 Da LogP -2.13 TPSA 150.3	✓ Ro5	✓ Clean	`C([C@H]([C@@H](C(=O)O)N)O)OP(=O)(O)O`
POP RCSB PDB	6E85	A0A1Y0PY16	176.0 Da LogP -2.08 TPSA 129.9	✓ Ro5	✓ Clean	`O[P@@](=O)([O-])O[P@@](=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
ZINC12501558 ZINC	0.594	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(…`
ZINC12501560 ZINC	0.594	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O…`
ZINC12501562 ZINC	0.594	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)…`
ZINC12501564 ZINC	0.594	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(…`
ZINC1532623 ZINC	0.594	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(…`
ZINC2047359 ZINC	0.594	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)COP(=O…`
ZINC2545091 ZINC	0.594	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O…`
ZINC3869602 ZINC	0.594	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)COP(=…`
ZINC3869603 ZINC	0.594	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)COP(=O…`
ZINC3869604 ZINC	0.594	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC4887586 ZINC	0.545	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887587 ZINC	0.545	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887588 ZINC	0.545	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887589 ZINC	0.545	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC5975509 ZINC	0.533	202.1 Da LogP -2.19 TPSA 127.5	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H](O)[C@H](O)CO`
ZINC100657408 ZINC	0.529	259.2 Da LogP -3.30 TPSA 170.5	1 viol.	✓ Clean	`N[C@H](C=O)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC215934438 ZINC	0.529	259.2 Da LogP -3.30 TPSA 170.5	1 viol.	✓ Clean	`N[C@H](C=O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC255961849 ZINC	0.529	259.2 Da LogP -3.30 TPSA 170.5	1 viol.	✓ Clean	`N[C@H](C=O)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC255961850 ZINC	0.529	259.2 Da LogP -3.30 TPSA 170.5	1 viol.	✓ Clean	`N[C@H](C=O)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC5132021 ZINC	0.529	259.2 Da LogP -3.30 TPSA 170.5	1 viol.	✓ Clean	`N[C@@H](C=O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1529626 ZINC	0.515	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC1532567 ZINC	0.515	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1532851 ZINC	0.515	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC30320708 ZINC	0.515	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC3870277 ZINC	0.515	310.1 Da LogP -2.50 TPSA 191.0	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1532601 ZINC	0.500	200.1 Da LogP -1.98 TPSA 124.3	✓ Ro5	✓ Clean	`O=C[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC2516111 ZINC	0.500	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)CO`
ZINC2522704 ZINC	0.500	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC32786787 ZINC	0.500	200.1 Da LogP -1.98 TPSA 124.3	✓ Ro5	✓ Clean	`O=C[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC3869233 ZINC	0.500	266.0 Da LogP -1.34 TPSA 170.8	✓ Ro5	✓ Clean	`O=C(O)[C@H](COP(=O)(O)O)OP(=O)(O)O`
ZINC3869234 ZINC	0.500	266.0 Da LogP -1.34 TPSA 170.8	✓ Ro5	✓ Clean	`O=C(O)[C@@H](COP(=O)(O)O)OP(=O)(O)O`
ZINC3869812 ZINC	0.500	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC5830339 ZINC	0.500	231.1 Da LogP -2.68 TPSA 156.5	1 viol.	✓ Clean	`O=C(NO)[C@H](O)[C@H](O)COP(=O)(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 A6T7I3

Pathways

KEGG R05837 BioCyc RXN-13179