Protein target profile

KP13_03430

Choline dehydrogenase

Genome: KpKP13 Gene: AHE45805.1 betA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GL29
Length 554
Pocket druggability 0.877
Direct ligand evidence 0 57 total records
Functional annotation 2 EC 6 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 (%)
47.849 Lower values reduce human off-target concern.
Human E-value
4.62e-171
Gut microbiome similarity
1.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
96.02 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 0.877
Structure A0A0H3GL29
Pocket Pocket 1
P2Rank 0.983
Structure A0A0H3GL29
Pocket Pocket 1
ColabFold model
FPocket 0.992 · Pocket 1
P2Rank 0.991 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 91 / 4744 genomes with a hit
Prevalence 1.9%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MQFDYIIIGAGSAGNVLATRLTEDPNTTVLLLEAGGPDYRFDFRTQMPAALAYPLQGKRYNWAYETEPEPYMNNRRMECGRGKGLGGSSLINGMCYIRGNAMDLDNWAKEPGLEHWSYLDCLPYYRKAETRDIGPNDYHGGDGPVSVTTPKPGNNPLFEAMVEAGVQAGYPRTDDLNGYQQEGFGPMDRTVTPQGRRTSTARGYLDQARGRPNLTIRTHALTDHIIFAGKRAVGVEWLEGESTIPSKATANKEVLLCAGAIASPQILQRSGVGNPELLRQFDIPVVHDLPGVGENLQDHLEMYLQYECKEPVSLYPALQWWNQPKIGAEWLFGGTGIGASNQFEAGGFIRSRAEFAWPNIQYHFLPVAINYNGSNAVKEHGFQCHVGSMRSPSRGHVRLKSRDPHAHPAILFNYMSHEQDWQEFRDAIRITREIMNQPALDKYRGREISPGIECQSDAELDEFVRNHAETAFHPCGTCKMGYDEMAVVDGEGRVHGLEGLRVVDASIMPQIITGNLNATTIMIGEKMADAIRGRQPLPRSTATYYVAGDAPVRR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 6 GO

Enzyme Commission (EC)

2

Gene Ontology (GO)

6
  • GO:0019285 The chemical reactions and pathways resulting in the formation of betaine (N-trimethylglycine) from the oxidation of choline.
  • GO:0016614 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
  • GO:0008812 Catalysis of the reaction: A + choline = AH(2) + betaine aldehyde.
  • GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • 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.

22 records
Show feature table
Start End DB Term Name
82 105 ProSitePatterns PS00623 GMC oxidoreductases signature 1.
82 105 InterPro IPR000172 Glucose-methanol-choline oxidoreductase, N-terminal
259 273 ProSitePatterns PS00624 GMC oxidoreductases signature 2.
259 273 InterPro IPR000172 Glucose-methanol-choline oxidoreductase, N-terminal
1 535 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
1 535 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
1 538 PIRSF PIRSF000137 Alcohol_oxidase
1 538 InterPro IPR012132 Glucose-methanol-choline oxidoreductase
3 539 PANTHER PTHR11552 GLUCOSE-METHANOL-CHOLINE GMC OXIDOREDUCTASE
3 539 InterPro IPR012132 Glucose-methanol-choline oxidoreductase
1 554 Hamap MF_00750 Oxygen-dependent choline dehydrogenase [betA].
1 554 InterPro IPR011533 Oxygen-dependent choline dehydrogenase
295 477 SUPERFAMILY SSF54373 FAD-linked reductases, C-terminal domain
3 300 Pfam PF00732 GMC oxidoreductase
3 300 InterPro IPR000172 Glucose-methanol-choline oxidoreductase, N-terminal
393 527 Pfam PF05199 GMC oxidoreductase
393 527 InterPro IPR007867 Glucose-methanol-choline oxidoreductase, C-terminal
4 537 NCBIfam TIGR01810 choline dehydrogenase
4 537 InterPro IPR011533 Oxygen-dependent choline dehydrogenase
43 472 Gene3D G3DSA:3.30.560.10 Glucose Oxidase, domain 3
4 525 Gene3D G3DSA:3.50.50.60 -
4 525 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily

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 #1
0.877
Likely same site as P2Rank 1 0.8 Å 44 shared residues 96% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #2
0.777
Likely same site as P2Rank 2 2.2 Å 24 shared residues 100% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.983
Likely same site as FPocket 1 0.8 Å 44 shared residues 96% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.77
Likely same site as FPocket 2 2.2 Å 24 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.098
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.05
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.047
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:473-473 Proton acceptor
UniProt: Binding site:4-33
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_A0A0H3GL29
AlphaFold DB full sequence Viewing
ColabFold KP13_03430
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.

57 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ANN PDB via homolog 152.1 Da · LogP 1.39 · TPSA 46.5 Open detail RCSB PDB
BET PDB via homolog Detail RCSB PDB
FAO PDB via homolog Detail RCSB PDB
FDA PDB via homolog Detail RCSB PDB
PLM 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
ANN RCSB PDB O94219 152.1 Da LogP 1.39 TPSA 46.5 ✓ Ro5 ✓ Clean COc1ccc(cc1)C(=O)O
BET RCSB PDB Q7X2H8 118.2 Da LogP -0.22 TPSA 37.3 ✓ Ro5 ✓ Clean C[N+](C)(C)CC(=O)O
FAO RCSB PDB Q7X2H8 789.6 Da LogP -2.56 TPSA 355.8 3 viol. ✓ Clean Cc1cc2c(cc1C)[N@@]([C@@H]3[C@H](N2)C(=O)NC(=O)N…
FDA RCSB PDB B8MX95 787.6 Da LogP -1.75 TPSA 363.3 3 viol. ✓ Clean Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C…
PLM RCSB PDB A0A248QE08 256.4 Da LogP 5.55 TPSA 37.3 1 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)O
PXM RCSB PDB Q5NT46 168.2 Da LogP 0.05 TPSA 79.4 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)CO)CN)O
STE RCSB PDB A0A248QE08 284.5 Da LogP 6.33 TPSA 37.3 1 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=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.