KpATCC43816 Protein target profile

L-2,4-diaminobutyrate decarboxylase

Accession: VK055_0686

Gene: AIK79309.1 ddc 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GNN7
Length 490
Pocket druggability (P2Rank · AlphaFold DB model) 0.715
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 55 total records
Functional annotation 0 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 (%)
48.958 Lower values reduce human off-target concern.
Human E-value
1.62e-23
Gut microbiome similarity
1.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
95.77 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) 0.715
Structure A0A0H3GNN7
Pocket Pocket 1
Druggability (FPocket) 0.636
Structure A0A0H3GNN7
Pocket Pocket 10
ColabFold model
P2Rank 0.778 · Pocket 1
FPocket 0.777 · Pocket 7
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 72 / 4744 genomes with a hit
Prevalence 1.5%

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 92.0% of genes in this genome.

Relative network centrality 92.0% more central than 92.0% of genes in this genome
Chokepoint Not a chokepoint
Catalyzed reaction

1 reaction mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSTLNPILAGSAQSVEAYQQVIEQTSQAVVQWLKQPEMYQGKSVDELRERISLEFNEQGLGNQAAIDRAIEYFLKDSLSVHHPQCVAHLHCPSLVISQAAEVLINATNQSMDSWDQSPSATIIEMKLIEWLRARVGFPAGDAGVFTSGGTQSNLMGLMLARDAFFARQGHSIQQDGLPGDIRKYKVLCSENAHFSVQKNMALMGLGYRSVTLVKTDEFARMDVSDLQAKIAQAQANGEQIMAIVATAGTTDAGAIDPLRDIAGIAAEHQIWLHVDAAWGGALLLSEQYRDYLDGLELVDSVTLDFHKQFFQTISCGAFLLKDARHYELMRYQAAYLNSEFDEEHGVPNLVSKSLQTTRRFDALKLWMGLEALGQKQYAAIIDHGVTMAKNVAEYVKSQPTLELVMQPQLASVLFRSRPAQMAGSDAAVIALLNQRVGDALLASGRANVGVTEHNGVTCLKLTLLNPVVTLDDVKVLLNLVERTAQELLAQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

6
  • 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:0019752 The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
  • GO:0016830 Catalysis of the cleavage of C-C bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond.
  • 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0016831 Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

10 records
Show feature table
Start End DB Term Name
109 360 Gene3D G3DSA:3.40.640.10 -
109 360 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
470 490 Coils Coil Coil
65 416 Pfam PF00282 Pyridoxal-dependent decarboxylase conserved domain
65 416 InterPro IPR002129 Pyridoxal phosphate-dependent decarboxylase
16 486 PANTHER PTHR45677 GLUTAMATE DECARBOXYLASE-RELATED
85 482 CDD cd06450 DOPA_deC_like
40 484 Gene3D G3DSA:3.90.1150.170 -
16 487 SUPERFAMILY SSF53383 PLP-dependent transferases
16 487 InterPro IPR015424 Pyridoxal phosphate-dependent transferase

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.

Download VMD script Full viewer

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Drag to rotate — click the view, then scroll to zoom.

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
0.715
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Surrounding area
Pocket 2 P2Rank #2
0.118
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Surrounding area
Pocket 3 P2Rank #3
0.063
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Surrounding area
Pocket 4 P2Rank #4
0.019
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Surrounding area
Pocket 5 P2Rank #5
0.015
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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 #10
0.636
Show in viewer
Surrounding area
Pocket 2 FPocket #1
0.396
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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_A0A0H3GNN7
AlphaFold DB full sequence Viewing
ColabFold VK055_0686
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.

55 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2SU PDB via homolog 236.2 Da · LogP 1.46 · TPSA 79.1 Open detail RCSB PDB
3SO PDB via homolog Detail RCSB PDB
ABU PDB via homolog Detail RCSB PDB
PLZ PDB via homolog Detail RCSB PDB
PMP 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
2SU RCSB PDB A7B1V0 236.2 Da LogP 1.46 TPSA 79.1 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(c[nH]2)C[C@](CF)(C(=O)O)N
3SO RCSB PDB A7B1V0 402.3 Da LogP 3.01 TPSA 132.7 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)/C=C/C(=O)Cc2c[nH]c3c2…
ABU RCSB PDB D1C7D8 103.1 Da LogP -0.19 TPSA 63.3 ✓ Ro5 ✓ Clean C(CC(=O)O)CN
PLZ RCSB PDB Q99259 334.3 Da LogP 0.66 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNCCCC(=O)O)O
PMP RCSB PDB D1C7D8 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)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.