KpATCC43816 Protein target profile

argD

Accession: VK055_3730

Gene: AIK82284.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3H3Z1
Length 406
Pocket druggability (P2Rank · AlphaFold DB model) 0.58
Direct ligand evidence 0 57 total records
Functional annotation 0 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 (%)
38.571 Lower values reduce human off-target concern.
Human E-value
1.06e-07
Gut microbiome similarity
3.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
45.876 Higher values support similarity to known essential genes.
DEG E-value
2.49e-113 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
97.98 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) 0.58
Structure A0A0H3H3Z1
Pocket Pocket 1
Druggability (FPocket) 0.552
Structure A0A0H3H3Z1
Pocket Pocket 27
ColabFold model
P2Rank 0.522 · Pocket 1
FPocket 0.903 · Pocket 3
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 156 / 4744 genomes with a hit
Prevalence 3.3%

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.

MATEQPAITRATFDEVILPIYAPAEFIPVKGKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVAALHQQGETLWHTSNVFTNEPALRLGRKLVEATFAERVVFMNSGTEANETAFKLARHYAVTRHSPYKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIVHVPFNDLQAVKAVMDDHTCAVVVEPIQGEGGVTAATPAFLQGLCELCDQHQALLVFDEVQCGMGRTGSLFAYMHYGVTPDILTSAKALGGGFPVSAMLTTHEIASAFHAGSHGSTYGGNPLACAVANAAFDLINTPAVLDGVSAKRELFVKHLQRLDAEFDLFSDIRGMGLLIGAELKPQHKGRARDFLYAAADAGVMVLNAGPDVMRFVPSLIIDEQDITEGMARFTQAVAKVING

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

5
  • 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:0006525 The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
  • GO:0008483 Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
  • GO:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
  • GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
60 305 Gene3D G3DSA:3.40.640.10 -
60 305 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
30 393 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
30 393 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
173 403 PIRSF PIRSF000521 Transaminase_4ab_Lys_Orn
173 403 InterPro IPR005814 Aminotransferase class-III
28 157 PIRSF PIRSF000521 Transaminase_4ab_Lys_Orn
28 157 InterPro IPR005814 Aminotransferase class-III
223 260 ProSitePatterns PS00600 Aminotransferases class-III pyridoxal-phosphate attachment site.
223 260 InterPro IPR005814 Aminotransferase class-III
26 400 Pfam PF00202 Aminotransferase class-III
26 400 InterPro IPR005814 Aminotransferase class-III
20 400 SUPERFAMILY SSF53383 PLP-dependent transferases
20 400 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
60 305 FunFam G3DSA:3.40.640.10:FF:000004 Acetylornithine aminotransferase
16 403 Hamap MF_01107 Acetylornithine/succinyldiaminopimelate aminotransferase [argD].
16 403 InterPro IPR004636 Acetylornithine/Succinylornithine transaminase family
21 400 CDD cd00610 OAT_like
21 400 InterPro IPR005814 Aminotransferase class-III
14 402 PANTHER PTHR11986 AMINOTRANSFERASE CLASS III
17 400 NCBIfam TIGR00707 acetylornithine/succinylornithine family transaminase
17 400 InterPro IPR004636 Acetylornithine/Succinylornithine transaminase family
8 404 NCBIfam TIGR03246 acetylornithine/succinylornithine family transaminase
8 404 InterPro IPR017652 Acetyl/Succinylornithine transaminase family, bacteria

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
0.58
Likely same site as FPocket 27 3.1 Å 11 shared residues 100% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.522
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Surrounding area
Pocket 3 P2Rank #3
0.283
Likely same site as FPocket 13 2.7 Å 9 shared residues 100% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.053
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Surrounding area
Pocket 5 P2Rank #5
0.047
Likely same site as FPocket 3 3.4 Å 8 shared residues 100% of smaller site
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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 #27
0.552
Likely same site as P2Rank 1 3.1 Å 11 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #13
0.341
Likely same site as P2Rank 3 2.7 Å 9 shared residues 100% of smaller site
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Surrounding area
Pocket 3 FPocket #3
0.294 Unusual size
Likely same site as P2Rank 5 3.4 Å 8 shared residues 100% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:108-109
UniProt: Binding site:141-141
UniProt: Binding site:144-144
UniProt: Binding site:226-229
UniProt: Binding site:283-283
UniProt: Binding site:284-284
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_A0A0H3H3Z1
AlphaFold DB full sequence Viewing
ColabFold VK055_3730
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 and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 6 0 loaded crystals
Measured bioactivity 1 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
P00 PDB via homolog 363.3 Da · LogP -0.14 · TPSA 184.8 Open detail RCSB PDB
POI PDB via homolog Detail RCSB PDB
PPE PDB via homolog Detail RCSB PDB
PXG PDB via homolog Detail RCSB PDB
SUO 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
P00 RCSB PDB P40732 363.3 Da LogP -0.14 TPSA 184.8 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/OCC[C@@H](C(=O)O)…
POI RCSB PDB Q5SHH5 405.3 Da LogP 0.16 TPSA 178.3 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNCCC[C@@H](C(=O)O)NC(…
PPE RCSB PDB Q5SHH5 379.3 Da LogP -0.47 TPSA 187.8 1 viol. ✓ Clean Cc1c(c(c(c[nH+]1)COP(=O)(O)O)CN[C@@H](CCC(=O)O)…
PXG RCSB PDB P40732 368.3 Da LogP 2.02 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNc2cccc(c2)C(=O)O)O
SUO RCSB PDB P77581 232.2 Da LogP -0.84 TPSA 129.7 ✓ Ro5 ✓ Clean C(C[C@@H](C(=O)O)NC(=O)CCC(=O)O)CN
TNF RCSB PDB P40732 229.1 Da LogP 1.12 TPSA 149.7 ✓ Ro5 ✓ Clean c1c(cc(c(c1[N+](=O)[O-])O)[N+](=O)[O-])[N+](=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.