Protein target profile

KP13_19569

Betaine aldehyde dehydrogenase

Genome: KpKP13 Gene: betB ANJ86619.1 3D evidence: Experimental + ColabFold model UniProt A0A0H3GTN1
Length 490
Pocket druggability 0.692
Direct ligand evidence 0 145 total records
Functional annotation 1 EC 5 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.

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 (%)
53.061 Lower values reduce human off-target concern.
Human E-value
3.72e-08
Gut microbiome similarity
1.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
44.375 Higher values support similarity to known essential genes.
DEG E-value
6.9e-139 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
98.49 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.692
Structure 7SWK
Pocket Pocket 2
P2Rank 0.958
Structure 7SWK
Pocket Pocket 1
ColabFold model
FPocket 0.95 · Pocket 3
P2Rank 0.988 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 92 / 4744 genomes with a hit
Prevalence 1.9%

Cross-references

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

Structure

Chemistry

ChEMBL CHEMBL4876602 ChEMBL CHEMBL4861872 ChEMBL CHEMBL4859904 ChEMBL CHEMBL4848258 ChEMBL CHEMBL4213331 ChEMBL CHEMBL4875157 ChEMBL CHEMBL4848831 ChEMBL CHEMBL4855442 ChEMBL CHEMBL4849624 ChEMBL CHEMBL4847114 ChEMBL CHEMBL4874309 ChEMBL A5Y ChEMBL CHEMBL4642789 ChEMBL CHEMBL4876076 ChEMBL CHEMBL4214509 ChEMBL CHEMBL4217452 ChEMBL CHEMBL4862833 ChEMBL CHEMBL4863668 ChEMBL CHEMBL4873315 ChEMBL CHEMBL4873090 ChEMBL CHEMBL1349972 ChEMBL CHEMBL4205216 ChEMBL CHEMBL4216790 ChEMBL CHEMBL4846491 ChEMBL CHEMBL4213859 ChEMBL CW2 ChEMBL CHEMBL4852411 ChEMBL CHEMBL4868666 ChEMBL CHEMBL4846203 ChEMBL CHEMBL5075900 ChEMBL CHEMBL1589630 ChEMBL CHEMBL4072941 ChEMBL CHEMBL5086460 ChEMBL CHEMBL5090970 ChEMBL CHEMBL449188 ChEMBL CHEMBL4217294 ChEMBL 6ZE ChEMBL CHEMBL5083058 ChEMBL CHEMBL4849586 ChEMBL CHEMBL4857551 ChEMBL CHEMBL4877915 ChEMBL CHEMBL4205099 ChEMBL CHEMBL5087589 ChEMBL CHEMBL4862473 ChEMBL CHEMBL4859854 ChEMBL CHEMBL4865571 ChEMBL CHEMBL4218404 ChEMBL CHEMBL4860590 ChEMBL CHEMBL494494 ChEMBL CHEMBL4205427 ChEMBL CHEMBL4213258 ChEMBL CHEMBL4846960 ChEMBL CHEMBL1562069 ChEMBL CHEMBL4214000 ChEMBL CHEMBL4866017 ChEMBL CHEMBL4871374 ChEMBL 3SR ChEMBL 3ST ChEMBL 3W9 ChEMBL CHEMBL1311611 ChEMBL CHEMBL1524501 ChEMBL CHEMBL2360124 ChEMBL CHEMBL3416557 ChEMBL CHEMBL3416558 ChEMBL CHEMBL3416559 ChEMBL CHEMBL3416560 ChEMBL CHEMBL3416561 ChEMBL CHEMBL4129274 ChEMBL CHEMBL4290215 ChEMBL CHEMBL4436671 ChEMBL CHEMBL4437559 ChEMBL CHEMBL4437739 ChEMBL CHEMBL4440588 ChEMBL CHEMBL4450023 ChEMBL CHEMBL4454424 ChEMBL CHEMBL4463367 ChEMBL CHEMBL4519005 ChEMBL CHEMBL4526691 ChEMBL CHEMBL455595 ChEMBL CHEMBL4564832 ChEMBL CHEMBL4566360 ChEMBL CHEMBL4579414 ChEMBL CHEMBL5169766 ChEMBL M39

Sequence

Primary amino-acid sequence viewer.

MSRMAEQQLYINGGYTSATSGRTFETINPATGEVLATVQAAGREDVDRAVESAQRGQKIWAAMTAMERSRILRRAVDLLRQRNDELARLETLDTGKPLSETAAVDIVTGADVLEYYAGLIPALEGSQIPLRDSSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTPLTALKLAEIYSEAGLPDGVFNVLPGIGAETGQYLTEHPDIAKISFTGGVASGKKVMANSAASSLKEVTMELGGKSPLIIADDADLDLAADIAMMANFYSSGQVCTNGTRVFVPAKQKAEFEHKILERVARIRPGDLFADDTNFGPLVSFPHRDNVLRYIESGKREGARLLCGGEALKGDGFDNGAWVAPTVFTDCSDEMTIVREEIFGPVMSILSYADEAEVIRRANATEYGLAAGVVTPNLNRAHRIIHQLEAGICWINSWGESPAEMPVGGYKHSGIGRENGVMTLQSYTQVKSIQVEMGKFQSIF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0019285 The chemical reactions and pathways resulting in the formation of betaine (N-trimethylglycine) from the oxidation of choline.
  • GO:0046872 Binding to a metal ion.
  • 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.
  • GO:0016620 Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
  • GO:0008802 Catalysis of the reaction: betaine aldehyde + NAD+ + H2O = betaine + NADH + H+.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
255 448 Gene3D G3DSA:3.40.309.10 Aldehyde Dehydrogenase; Chain A, domain 2
255 448 InterPro IPR016163 Aldehyde dehydrogenase, C-terminal
4 490 Hamap MF_00804 Betaine aldehyde dehydrogenase [betB].
4 490 InterPro IPR011264 Betaine aldehyde dehydrogenase
255 448 FunFam G3DSA:3.40.309.10:FF:000014 NAD/NADP-dependent betaine aldehyde dehydrogenase
10 477 NCBIfam TIGR01804 betaine-aldehyde dehydrogenase
10 477 InterPro IPR011264 Betaine aldehyde dehydrogenase
279 290 ProSitePatterns PS00070 Aldehyde dehydrogenases cysteine active site.
279 290 InterPro IPR016160 Aldehyde dehydrogenase, cysteine active site
11 279 FunFam G3DSA:3.40.605.10:FF:000007 NAD/NADP-dependent betaine aldehyde dehydrogenase
4 483 SUPERFAMILY SSF53720 ALDH-like
4 483 InterPro IPR016161 Aldehyde/histidinol dehydrogenase
17 479 Pfam PF00171 Aldehyde dehydrogenase family
17 479 InterPro IPR015590 Aldehyde dehydrogenase domain
10 478 Gene3D G3DSA:3.40.605.10 Aldehyde Dehydrogenase; Chain A, domain 1
10 478 InterPro IPR016162 Aldehyde dehydrogenase, N-terminal
7 482 PANTHER PTHR11699 ALDEHYDE DEHYDROGENASE-RELATED
26 484 CDD cd07090 ALDH_F9_TMBADH
251 258 ProSitePatterns PS00687 Aldehyde dehydrogenases glutamic acid active site.
251 258 InterPro IPR029510 Aldehyde dehydrogenase, glutamic acid active site

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 #2
0.692
Likely same site as P2Rank 1 1.1 Å 20 shared residues 91% of smaller site
Unusual size
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Surrounding area
Site 2 FPocket #4
0.579
Likely same site as P2Rank 3 1.5 Å 9 shared residues 100% of smaller site
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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
0.958
Likely same site as FPocket 2 1.1 Å 20 shared residues 91% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.913
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Surrounding area
Site 3 P2Rank #3
0.057
Likely same site as FPocket 4 1.5 Å 9 shared residues 100% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.017
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.014
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Surrounding area
All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 1

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
PDB 7SWK
X-ray 1.80 Å A,B
100.0% 1-490
Viewing
ColabFold KP13_19569
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.

145 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 95 records from similar proteins
Structural ligands 11 0 loaded crystals
Measured bioactivity 84 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
7PE PDB via homolog 310.4 Da · LogP 0.10 · TPSA 75.6 Open detail RCSB PDB
DTT PDB via homolog Detail RCSB PDB
KXT PDB via homolog Detail RCSB PDB
N4Q PDB via homolog Detail RCSB PDB
N98 PDB via homolog Detail RCSB PDB

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
7PE RCSB PDB Q9HTJ1 310.4 Da LogP 0.10 TPSA 75.6 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCCOCCO
DTT RCSB PDB Q9HTJ1 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
KXT RCSB PDB P47895 270.3 Da LogP 4.67 TPSA 17.3 ✓ Ro5 ✓ Clean c1ccc(cc1)c2ccc3nc(cn3c2)c4ccccc4
N4Q RCSB PDB P47895 360.4 Da LogP 4.69 TPSA 45.0 ✓ Ro5 ✓ Clean COc1ccc(cc1)c2cn3cc(ccc3n2)c4cc(cc(c4)OC)OC
N98 RCSB PDB P47895 373.4 Da LogP 3.58 TPSA 75.0 ✓ Ro5 ✓ Clean COC(=O)c1cc(nc2n1nc(c2)c3ccccc3)c4ccc5c(c4)OCO5
NW8 RCSB PDB P47895 304.8 Da LogP 5.32 TPSA 17.3 1 viol. ✓ Clean c1ccc(cc1)c2cn3cccc(c3n2)c4ccc(cc4)Cl
PE4 RCSB PDB Q9HTJ1 354.4 Da LogP 0.11 TPSA 84.8 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCCOCCOCCO
REA RCSB PDB P47895 300.4 Da LogP 5.60 TPSA 37.3 1 viol. ✓ Clean CC1=C(C(CCC1)(C)C)/C=C/C(=C/C=C/C(=C/C(=O)O)/C)…
SIN RCSB PDB Q3JLL8 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
TOE RCSB PDB Q9HTJ1 164.2 Da LogP -0.34 TPSA 47.9 ✓ Ro5 ✓ Clean COCCOCCOCCO
TXE RCSB PDB Q9HTJ1 667.5 Da LogP -2.95 TPSA 317.6 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.