KpATCC43816 Protein target profile

dimethyl sulfoxide reductase, chain A

Accession: VK055_0920

Gene: AIK79543.1 dmsA 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GMZ1
Length 811
Pocket druggability (P2Rank · AlphaFold DB model) 0.966
Direct ligand evidence 0 63 total records
Functional annotation 0 EC 9 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
No hit
Gut microbiome similarity
3.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
63.772 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
92.99 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) 0.966
Structure A0A0H3GMZ1
Pocket Pocket 1
Druggability (FPocket) 0.909
Structure A0A0H3GMZ1
Pocket Pocket 2
ColabFold model
P2Rank 0.975 · Pocket 1
FPocket 0.954 · Pocket 2
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 152 / 4744 genomes with a hit
Prevalence 3.2%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

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.

MSNQESPGGVSRRALLKSTALGSLALAAGGLTLPFTLRRAAAAVQQATGDTTRIVWGACSVNCGSRCALRLHVRDDEVVYVETDNTGDDRYGDHQVRACLRGRSIRRRINHPDRLNYPMKRVGKRGEGKFVRISWQEALDTLADRLKSVVAQYGNEAVYINYSSGIVGGNITRSSPSASPVARLMNCYGGSLNQYGTYSTAQIACAMPYTYGSNDGNSTSDIENSKLVVMFGNNPAETRMSGGGITWYLEQARERSNARMIVIDPRYTDTAAGREDEWIPIRPGTDAALVAGIAWVLINEDLVDQPFLDKYCVGYDEKTLPAGAPANGHYKAYILGEGDDGIAKTPQWASRITGIPTDRIIKLAREIGMSKPAYICQGWGPQRQANGELTARAIAMLPILTGNVGINGGNSGARESTYTITIERLPVLENPVKTAISCFTWTDAIARGPEMTASRDGVRGKEKLDVPIKFLWNYAGNTIINQHSDINKTHEILQEESKCETIVVIDNFMTSSAKYADLLLPDLMTVEQEDIIPNDYAGNMGYLIFIQPATSAKFERKPIYWILSEVAKRLGDDVHQRFTEGRTQEQWLQYLYAKMVAKDPVLPAYEDLKRMGIYKRKDPNGHFVAYRDFRRDPEAHPLKTPSGKIEIYSSRLAEIAARWQLEKDEVISPLPVYASTFEGWDDPLRSQYPLQLFGFHYKARTHSSYGNVDVLQAACRQEVWINPLDAEKRGIKNGDMVRVFNQRGEVRLPAKVTPRIMPGVSAMGQGAWHDANMTGDRIDHGACMNTLTTHRPSPLAKGNPQHTNLVDIEKV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

9 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

9
  • GO:0030151 Binding to a molybdenum ion (Mo).
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0043546 Binding to a molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) coordinated by one or two molybdopterin ligands.
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0009389 Catalysis of the reaction: dimethyl sulfide + a menaquinone + H2O = dimethyl sulfoxide + a menaquinol.
  • GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0009055 A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways.
  • GO:0009061 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

36 records
Show feature table
Start End DB Term Name
665 811 Gene3D G3DSA:2.40.40.20 -
19 37 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 42 Phobius SIGNAL_PEPTIDE Signal peptide region
10 811 NCBIfam TIGR02166 anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family
10 811 InterPro IPR011888 Anaerobic dimethyl sulphoxide reductase, subunit A, DmsA/YnfE
38 42 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
206 649 Gene3D G3DSA:3.40.228.10 Dimethylsulfoxide Reductase, domain 2
1 18 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
680 811 SUPERFAMILY SSF50692 ADC-like
680 811 InterPro IPR009010 Aspartate decarboxylase-like domain superfamily
47 115 Gene3D G3DSA:2.20.25.90 -
688 810 CDD cd02794 MopB_CT_DmsA-EC
53 111 Pfam PF04879 Molybdopterin oxidoreductase Fe4S4 domain
53 111 InterPro IPR006963 Molybdopterin oxidoreductase, 4Fe-4S domain
410 618 FunFam G3DSA:3.40.50.740:FF:000015 Anaerobic dimethyl sulfoxide reductase subunit A
116 637 Gene3D G3DSA:3.40.50.740 -
56 679 CDD cd02770 MopB_DmsA-EC
665 811 FunFam G3DSA:2.40.40.20:FF:000010 Anaerobic dimethyl sulfoxide reductase subunit A
690 803 Pfam PF01568 Molydopterin dinucleotide binding domain
690 803 InterPro IPR006657 Molybdopterin dinucleotide-binding domain
1 42 ProSiteProfiles PS51318 Twin arginine translocation (Tat) signal profile.
1 42 InterPro IPR006311 Twin-arginine translocation pathway, signal sequence
54 692 SUPERFAMILY SSF53706 Formate dehydrogenase/DMSO reductase, domains 1-3
52 111 SMART SM00926 Molybdop_Fe4S4_2
52 111 InterPro IPR006963 Molybdopterin oxidoreductase, 4Fe-4S domain
726 753 ProSitePatterns PS00932 Prokaryotic molybdopterin oxidoreductases signature 3.
726 753 InterPro IPR006655 Molybdopterin oxidoreductase, prokaryotic, conserved site
124 337 FunFam G3DSA:3.40.50.12440:FF:000003 Anaerobic dimethyl sulfoxide reductase subunit A
10 811 PANTHER PTHR43742 TRIMETHYLAMINE-N-OXIDE REDUCTASE
206 429 FunFam G3DSA:3.40.228.10:FF:000004 Dimethyl sulfoxide reductase subunit A
52 113 ProSiteProfiles PS51669 Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.
52 113 InterPro IPR006963 Molybdopterin oxidoreductase, 4Fe-4S domain
53 123 FunFam G3DSA:3.40.50.12440:FF:000002 Anaerobic dimethyl sulfoxide reductase, A subunit
43 811 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
114 569 Pfam PF00384 Molybdopterin oxidoreductase
114 569 InterPro IPR006656 Molybdopterin oxidoreductase

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
0.966
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Surrounding area
Pocket 2 P2Rank #2
0.161
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Surrounding area
Pocket 3 P2Rank #3
0.143
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Surrounding area
Pocket 4 P2Rank #4
0.108
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Surrounding area
Pocket 5 P2Rank #5
0.106
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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 #2
0.909
Show in viewer
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_A0A0H3GMZ1
AlphaFold DB full sequence Viewing
ColabFold VK055_0920
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.

63 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 13 records from similar proteins
Structural ligands 13 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2MD PDB via homolog 742.6 Da · LogP -2.53 · TPSA 346.6 Open detail RCSB PDB
2MO PDB via homolog Detail RCSB PDB
4MO PDB via homolog Detail RCSB PDB
6MO PDB via homolog Detail RCSB PDB
6WO 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
2MD RCSB PDB O87948 742.6 Da LogP -2.53 TPSA 346.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=…
2MO RCSB PDB Q52675 127.9 Da LogP -0.24 TPSA 34.1 ✓ Ro5 ✓ Clean O=[Mo]=O
4MO RCSB PDB Q52675 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo+4]
6MO RCSB PDB Q52675 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo+6]
6WO RCSB PDB Q52675 199.8 Da LogP -0.12 TPSA 17.1 ✓ Ro5 ✓ Clean O=[W+4]
MGD RCSB PDB Q7WTU0 740.6 Da LogP -2.06 TPSA 346.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=…
MO RCSB PDB Q7WTU0 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo]
NO2 RCSB PDB P07658 46.0 Da LogP 0.25 TPSA 52.5 ✓ Ro5 ✓ Clean N(=O)[O-]
O RCSB PDB Q52675 18.0 Da LogP -0.82 TPSA 31.5 ✓ Ro5 ✓ Clean O
PG5 RCSB PDB Q7WTU0 178.2 Da LogP 0.31 TPSA 36.9 ✓ Ro5 ✓ Clean COCCOCCOCCOC
PGD RCSB PDB Q52675 738.6 Da LogP -2.97 TPSA 343.0 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=…
SO2 RCSB PDB Q52675 64.1 Da LogP -0.67 TPSA 34.1 ✓ Ro5 ✓ Clean O=S=O
W RCSB PDB Q71EW5 183.8 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [W+6]

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.