KpATCC43816 Protein target profile

superoxide dismutase (Mn)

Accession: VK055_3260

Gene: sodA AIK81821.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GLE8
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Length 206
Pocket druggability (P2Rank · AlphaFold DB model) 0.088
Metabolic reactions 2
Chokepoint No
Direct ligand evidence 0 5 total records
Functional annotation 1 EC 5 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 5 structural and 0 bioactivity records.

Risks to review

Human similarity Top human hit identity: 54.348%. Microbiome similarity 389 of 4744 screened genomes (8.2%) have a significant similarity hit. Mixed conservation Core/accessory calls are not fully concordant. Weak predicted binding pocket FPocket selected-pocket score 0.29.

Evidence coverage

Core evidence streams are available for this target.
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 (%)
54.348 Lower values reduce human off-target concern.
Human E-value
2.07e-11
Gut microbiome similarity
8.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
59.223 Higher values support similarity to known essential genes.
DEG E-value
1.06e-84 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) 0.088
Structure A0A0H3GLE8
Pocket Pocket 1
Druggability (FPocket) 0.293
Structure A0A0H3GLE8
Pocket Pocket 11
ColabFold model
P2Rank 0.039 · Pocket 1
FPocket 0.175 · Pocket 9
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 389 / 4744 genomes with a hit
Prevalence 8.2%

Metabolic context

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

Explore metabolic network
Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

Catalyzed reactions

2 reactions 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.

MSYTLPSLPYAYDALEPHFDKQTMEIHHTKHHQTYVNNANAALESLPEFANLSAEELITKLDQLPADKKTVLRNNAGGHANHSLFWKGLKTGTTLQGDLKAAIERDFGSVENFKAEFEKAAATRFGSGWAWLVLKGDKLAVVSTANQDSPLMGEAISGASGFPIIGLDVWEHAYYLKFQNRRPDYIKAFWDVVNWDEAAARFAAKK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization
Periplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0004784 Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + H2O2.
  • GO:0006801 The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.
  • GO:0046872 Binding to a metal ion.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0030145 Binding to a manganese ion (Mn).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

29 records
Show feature table
Start End DB Term Name
27 40 PRINTS PR01703 Manganese superoxide dismutase signature
27 40 InterPro IPR001189 Manganese/iron superoxide dismutase
124 132 PRINTS PR01703 Manganese superoxide dismutase signature
124 132 InterPro IPR001189 Manganese/iron superoxide dismutase
6 17 PRINTS PR01703 Manganese superoxide dismutase signature
6 17 InterPro IPR001189 Manganese/iron superoxide dismutase
73 86 PRINTS PR01703 Manganese superoxide dismutase signature
73 86 InterPro IPR001189 Manganese/iron superoxide dismutase
166 178 PRINTS PR01703 Manganese superoxide dismutase signature
166 178 InterPro IPR001189 Manganese/iron superoxide dismutase
2 89 Pfam PF00081 Iron/manganese superoxide dismutases, alpha-hairpin domain
2 89 InterPro IPR019831 Manganese/iron superoxide dismutase, N-terminal
1 90 SUPERFAMILY SSF46609 Fe,Mn superoxide dismutase (SOD), N-terminal domain
1 90 InterPro IPR036324 Manganese/iron superoxide dismutase, N-terminal domain superfamily
95 204 SUPERFAMILY SSF54719 Fe,Mn superoxide dismutase (SOD), C-terminal domain
95 204 InterPro IPR036314 Manganese/iron superoxide dismutase, C-terminal domain superfamily
96 201 Pfam PF02777 Iron/manganese superoxide dismutases, C-terminal domain
96 201 InterPro IPR019832 Manganese/iron superoxide dismutase, C-terminal
20 90 Gene3D G3DSA:1.10.287.990 Fe,Mn superoxide dismutase (SOD) domain
20 90 InterPro IPR036324 Manganese/iron superoxide dismutase, N-terminal domain superfamily
1 205 PANTHER PTHR43595 37S RIBOSOMAL PROTEIN S26, MITOCHONDRIAL
1 206 PIRSF PIRSF000349 MnSOD_FeSOD
1 206 InterPro IPR001189 Manganese/iron superoxide dismutase
168 175 ProSitePatterns PS00088 Manganese and iron superoxide dismutases signature.
168 175 InterPro IPR019833 Manganese/iron superoxide dismutase, binding site
89 206 FunFam G3DSA:3.55.40.20:FF:000001 Superoxide dismutase
20 90 FunFam G3DSA:1.10.287.990:FF:000001 Superoxide dismutase
95 206 Gene3D G3DSA:3.55.40.20 -
95 206 InterPro IPR036314 Manganese/iron superoxide dismutase, C-terminal 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 · P2Rank

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

Pocket 1 P2Rank #1
0.088
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Surrounding area
Pocket 2 P2Rank #2
0.053
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Surrounding area
Pocket 3 P2Rank #3
0.01
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Surrounding area
Pocket 4 P2Rank #4
0.0
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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 #11
0.293
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Surrounding area
Residue sets
UniProt: Binding site:168-168
UniProt: Binding site:172-172
UniProt: Binding site:27-27
UniProt: Binding site:82-82
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_A0A0H3GLE8
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_3260
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.

5 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 0 similarity-based ZINC candidates
Best available ligand signal
AZI PDB via homolog 42.0 Da · LogP 0.87 · TPSA 58.7 Open detail RCSB PDB
MH2 PDB via homolog Detail RCSB PDB
MLI PDB via homolog Detail RCSB PDB
O PDB via homolog Detail RCSB PDB
PEO 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
AZI RCSB PDB
1ZLZ
P00448 42.0 Da LogP 0.87 TPSA 58.7 ✓ Ro5 Alert [N-]=[N+]=[N-]
MH2 RCSB PDB
1IXB
P00448 71.9 Da LogP -0.56 TPSA 20.2 ✓ Ro5 ✓ Clean O[Mn+2]
MLI RCSB PDB
3DC5
P41977 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
O RCSB PDB
2NYB
P0AGD3 18.0 Da LogP -0.82 TPSA 31.5 ✓ Ro5 ✓ Clean O
PEO RCSB PDB
3K9S
P00448 34.0 Da LogP 0.02 TPSA 40.5 ✓ Ro5 ✓ Clean OO

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.

Sequence

UniProt A0A0H3GLE8

Pathways

BioCyc SUPEROX-DISMUT-RXN[CCO-PERI-BAC]-SUPER-OXIDE/PROTON//HYDROGEN-PEROXIDE/OXYGEN-MOLECULE.68. BioCyc SUPEROX-DISMUT-RXN[CCO-CYTOSOL]-SUPER-OXIDE/PROTON//HYDROGEN-PEROXIDE/OXYGEN-MOLECULE.67.