KpATCC43816 Protein target profile
orn/Lys/Arg decarboxylase, N-terminal domain protein
Accession: VK055_4078
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
Evidence coverage
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 modelP2Rank'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.
Sequence
Primary amino-acid sequence viewer.
MKSMHIAASCELVTRLSTHRRVVALDSTDFTDVAAVVISAADSRSGILTLLRRSGFNLPVYLLSETAVDKPEGVQAVIAGKDQEWLELEAAACDYEARLLPPFFNTLTQYVEMDNSTFACPGHQHGAFFKKHPAGRQFYDFFGENVFRADMCNADVKLGDLLIHEGSAKHAQKFAAKVFNADKTYFVLNGTSAANKVVTNALLTRGDLVLFDRNNHKSNHHGALIQAGATPVYLEAARNPFGFIGGIDERCFDEHYLRDLIREAAPEKANASRPFRLAVIQLGTYDGTVYNARQVVDKIGHLCDYILFDSAWVGYEQFIPMMADCSPLLLELTPDDPGIFVTQSVHKQQAGFSQTSQIHKKDNHLRGQARFCPHKRLNNAFMLHASTSPFYPLFAALDVNAKIHEGESGRRLWAECVALGIEARKAIIANCKMIQPFIPPTVAGRPWQDHPTEAIARERRFFSFEPGARWHGFEGYADDQYFVDPCKLLLTTPGIDAESGEYSEFGIPATILAHYLRENGIVPEKCDLNSILFLLTPAESAEKMAQLVAMLGQFEQHIEADTPLADVLPTIYNKYPVRYRDYTLRELCQEMHDLYVSFDVKSLQKEMFRKRSFPRVVMNPQDANHEFIRGNVELVRLSEAEGRVAAEGALPYPPGVLCVVPGEVWGGAVLRYFLALEEGVNMLPGFSPELQGVYSETDPDGIKRLYGYVLKG
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Subcellular localization
- Localization
- Cytoplasmic
Enzyme Commission (EC)
1Gene 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.
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.
How colors and pocket overlays are used
Pocket details Inspect a specific pocket, or open the full viewer
- Method
- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
Selecting a pocket opens its details and centers the viewer without clearing other active layers. Use Focus this pocket when you want to hide the rest; use Surface for the wider residue environment.
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
All structural evidence
Structural evidence
0 + 2Experimental 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.
Structural ligand evidence is available for this target.
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.
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 |
|---|---|---|---|---|---|
| ZINC12501520 ZINC | 1.000 | 458.5 Da LogP -0.88 TPSA 123.5 | 1 viol. | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC3874716 ZINC | 1.000 | 414.5 Da LogP -0.90 TPSA 114.3 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC4283769 ZINC | 1.000 | 238.3 Da LogP -0.96 TPSA 77.4 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCO
|
| ZINC4521548 ZINC | 1.000 | 282.3 Da LogP -0.95 TPSA 86.6 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCO
|
| ZINC5178829 ZINC | 1.000 | 326.4 Da LogP -0.93 TPSA 95.8 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCO
|
| ZINC5178830 ZINC | 1.000 | 370.4 Da LogP -0.91 TPSA 105.1 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC104869865 ZINC | 0.836 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O…
|
| ZINC12504289 ZINC | 0.836 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…
|
| ZINC34541308 ZINC | 0.836 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…
|
| ZINC35000839 ZINC | 0.836 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…
|
| ZINC45284491 ZINC | 0.836 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…
|
| ZINC80639694 ZINC | 0.836 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…
|
| ZINC8215481 ZINC | 0.836 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…
|
| ZINC12503703 ZINC | 0.738 | 427.2 Da LogP -1.42 TPSA 232.3 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@@H](CO[P@@](=O)(…
|
| ZINC8215878 ZINC | 0.738 | 427.2 Da LogP -1.42 TPSA 232.3 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O…
|
| ZINC12503440 ZINC | 0.719 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](OP(=O)(O)O)…
|
| ZINC1530370 ZINC | 0.719 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@H](OP(=O)(O)O)[…
|
| ZINC28631009 ZINC | 0.719 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@H](OP(=O)(O)O)[…
|
| ZINC3872740 ZINC | 0.719 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O)…
|
| ZINC3872741 ZINC | 0.719 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O…
|
| ZINC3872742 ZINC | 0.719 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O)…
|
| ZINC3872743 ZINC | 0.719 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O…
|
| ZINC12501413 ZINC | 0.714 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…
|
| ZINC12958448 ZINC | 0.714 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…
|
| ZINC1532555 ZINC | 0.714 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…
|
| ZINC16546189 ZINC | 0.714 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…
|
| ZINC2159505 ZINC | 0.714 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…
|
| ZINC3073318 ZINC | 0.714 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…
|
| ZINC3869963 ZINC | 0.714 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…
|
| ZINC3869965 ZINC | 0.714 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…
|
| ZINC9334496 ZINC | 0.714 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…
|
| ZINC115086873 ZINC | 0.688 | 209.2 Da LogP -1.08 TPSA 83.2 | ✓ Ro5 | ✓ Clean |
NOCCOCCOCCOCCO
|
| ZINC137432264 ZINC | 0.688 | 457.6 Da LogP -0.91 TPSA 129.3 | 1 viol. | ✓ Clean |
NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC146143823 ZINC | 0.688 | 237.3 Da LogP -1.00 TPSA 83.2 | ✓ Ro5 | ✓ Clean |
NCCOCCOCCOCCOCCO
|
| ZINC1542984442 ZINC | 0.688 | 413.5 Da LogP -0.93 TPSA 120.1 | ✓ Ro5 | ✓ Clean |
NCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC1565503710 ZINC | 0.688 | 254.3 Da LogP -0.03 TPSA 57.2 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCS
|
| ZINC1580161 ZINC | 0.688 | 208.3 Da LogP -0.33 TPSA 57.2 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCO
|
| ZINC16052118 ZINC | 0.688 | 340.4 Da LogP -0.28 TPSA 84.8 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCOCCO
|
| ZINC1857792028 ZINC | 0.688 | 430.6 Da LogP 0.04 TPSA 94.1 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCOCCS
|
| ZINC1857792057 ZINC | 0.688 | 474.6 Da LogP 0.06 TPSA 103.3 | 1 viol. | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS
|
| ZINC230494776 ZINC | 0.688 | 325.4 Da LogP -0.96 TPSA 101.6 | ✓ Ro5 | ✓ Clean |
NCCOCCOCCOCCOCCOCCOCCO
|
| ZINC34317654 ZINC | 0.688 | 472.6 Da LogP -0.23 TPSA 112.5 | 1 viol. | ✓ Clean |
COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC44076059 ZINC | 0.688 | 428.5 Da LogP -0.24 TPSA 103.3 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC5210101 ZINC | 0.688 | 252.3 Da LogP -0.31 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCO
|
| ZINC5650743 ZINC | 0.688 | 222.3 Da LogP 0.07 TPSA 57.2 | ✓ Ro5 | ✓ Clean |
CCOCCOCCOCCOCCO
|
| ZINC5997860 ZINC | 0.688 | 296.4 Da LogP -0.29 TPSA 75.6 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCO
|
| ZINC77271182 ZINC | 0.688 | 281.3 Da LogP -0.98 TPSA 92.4 | ✓ Ro5 | ✓ Clean |
NCCOCCOCCOCCOCCOCCO
|
| ZINC83253921 ZINC | 0.688 | 369.5 Da LogP -0.95 TPSA 110.9 | ✓ Ro5 | ✓ Clean |
NCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC90741446 ZINC | 0.688 | 386.5 Da LogP 0.02 TPSA 84.8 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCS
|
| ZINC90741447 ZINC | 0.688 | 298.4 Da LogP -0.01 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCS
|
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.