KpATCC43816 Protein target profile

orn/Lys/Arg decarboxylase, N-terminal domain protein

Accession: VK055_4078

Gene: AIK82624.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GYC4
Length 712
Pocket druggability (P2Rank · AlphaFold DB model) 0.874
Direct ligand evidence 0 51 total records
Functional annotation 1 EC 8 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.

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
5.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
95.51 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) 0.874
Structure A0A0H3GYC4
Pocket Pocket 1
Druggability (FPocket) 0.724
Structure A0A0H3GYC4
Pocket Pocket 1
ColabFold model
P2Rank 0.89 · Pocket 1
FPocket 0.915 · Pocket 4
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 261 / 4744 genomes with a hit
Prevalence 5.5%

Metabolic context

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

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MKSMHIAASCELVTRLSTHRRVVALDSTDFTDVAAVVISAADSRSGILTLLRRSGFNLPVYLLSETAVDKPEGVQAVIAGKDQEWLELEAAACDYEARLLPPFFNTLTQYVEMDNSTFACPGHQHGAFFKKHPAGRQFYDFFGENVFRADMCNADVKLGDLLIHEGSAKHAQKFAAKVFNADKTYFVLNGTSAANKVVTNALLTRGDLVLFDRNNHKSNHHGALIQAGATPVYLEAARNPFGFIGGIDERCFDEHYLRDLIREAAPEKANASRPFRLAVIQLGTYDGTVYNARQVVDKIGHLCDYILFDSAWVGYEQFIPMMADCSPLLLELTPDDPGIFVTQSVHKQQAGFSQTSQIHKKDNHLRGQARFCPHKRLNNAFMLHASTSPFYPLFAALDVNAKIHEGESGRRLWAECVALGIEARKAIIANCKMIQPFIPPTVAGRPWQDHPTEAIARERRFFSFEPGARWHGFEGYADDQYFVDPCKLLLTTPGIDAESGEYSEFGIPATILAHYLRENGIVPEKCDLNSILFLLTPAESAEKMAQLVAMLGQFEQHIEADTPLADVLPTIYNKYPVRYRDYTLRELCQEMHDLYVSFDVKSLQKEMFRKRSFPRVVMNPQDANHEFIRGNVELVRLSEAEGRVAAEGALPYPPGVLCVVPGEVWGGAVLRYFLALEEGVNMLPGFSPELQGVYSETDPDGIKRLYGYVLKG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
  • 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:0016831 Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0004586 Catalysis of the reaction: L-ornithine + H+ = CO2 + putrescine.
  • GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
  • GO:0008295 The chemical reactions and pathways resulting in the formation of spermidine, N-(3-aminopropyl)-1,4-diaminobutane.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

31 records
Show feature table
Start End DB Term Name
593 712 FunFam G3DSA:3.90.100.10:FF:000001 Lysine decarboxylase, inducible
101 412 Gene3D G3DSA:3.40.640.10 -
101 412 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
4 79 Pfam PF03709 Orn/Lys/Arg decarboxylase, N-terminal domain
4 79 InterPro IPR005308 Orn/Lys/Arg decarboxylase, N-terminal
1 100 FunFam G3DSA:3.40.50.220:FF:000002 Ornithine decarboxylase, constitutive
593 712 Gene3D G3DSA:3.90.100.10 -
413 592 FunFam G3DSA:3.90.1150.10:FF:000032 Ornithine decarboxylase SpeF
101 412 FunFam G3DSA:3.40.640.10:FF:000008 Lysine decarboxylase, inducible
1 100 Gene3D G3DSA:3.40.50.220 -
1 100 InterPro IPR027464 Ornithine decarboxylase, N-terminal
102 428 CDD cd00615 Orn_deC_like
102 428 InterPro IPR000310 Orn/Lys/Arg decarboxylase, major domain
2 712 PIRSF PIRSF009393 Orn_decarb
2 712 InterPro IPR011193 Ornithine/lysine/arginine decarboxylase
101 543 Pfam PF01276 Orn/Lys/Arg decarboxylase, major domain
101 543 InterPro IPR000310 Orn/Lys/Arg decarboxylase, major domain
568 697 Pfam PF03711 Orn/Lys/Arg decarboxylase, C-terminal domain
568 697 InterPro IPR008286 Orn/Lys/Arg decarboxylase, C-terminal
563 711 SUPERFAMILY SSF55904 Ornithine decarboxylase C-terminal domain
563 711 InterPro IPR036633 Orn/Lys/Arg decarboxylase, C-terminal domain superfamily
101 558 SUPERFAMILY SSF53383 PLP-dependent transferases
101 558 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
342 356 ProSitePatterns PS00703 Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site.
342 356 InterPro IPR000310 Orn/Lys/Arg decarboxylase, major domain
9 711 PANTHER PTHR45229 CONSTITUTIVE ORNITHINE DECARBOXYLASE
9 711 InterPro IPR011193 Ornithine/lysine/arginine decarboxylase
413 592 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
413 592 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
1 100 SUPERFAMILY SSF52172 CheY-like
1 100 InterPro IPR011006 CheY-like 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 · P2Rank

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

Pocket 1 P2Rank #1
0.874
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Surrounding area
Pocket 2 P2Rank #2
0.32
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Surrounding area
Pocket 3 P2Rank #3
0.176
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Surrounding area
Pocket 4 P2Rank #4
0.157
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Surrounding area
Pocket 5 P2Rank #5
0.114
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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 #1
0.724
Show in viewer
Surrounding area
Pocket 2 FPocket #23
0.407
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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_A0A0H3GYC4
AlphaFold DB full sequence Viewing
ColabFold VK055_4078
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.

51 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 1 records from similar proteins
Structural ligands 1 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
G4P PDB via homolog 603.2 Da · LogP -2.22 · TPSA 345.6 Open detail RCSB PDB
ZINC12501520 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC3874716 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC4283769 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC4521548 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

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
G4P RCSB PDB P0A9H3 603.2 Da LogP -2.22 TPSA 345.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=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.