Genome KpKP13

Protein target profile

Anaerobic dimethyl sulfoxide reductase chain B

Accession: KP13_01159

Gene: AHE44739.1 dmsB 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GX32
Length 205
Pocket druggability (P2Rank · AlphaFold DB model) 0.037
Direct ligand evidence 0 65 total records
Functional annotation 0 EC 4 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.

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
4.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
88.293 Higher values support similarity to known essential genes.
DEG E-value
4.07e-141 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
96.99 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) 0.037
Structure A0A0H3GX32
Pocket Pocket 1
Druggability (FPocket) 0.385
Structure A0A0H3GX32
Pocket Pocket 2
ColabFold model
P2Rank 0.162 · Pocket 1
FPocket 0.542 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 215 / 4744 genomes with a hit
Prevalence 4.5%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MSTQYGFFIDSARCTGCKTCELACKDYKNLTPEVSFRRIYEYAGGDWQEDNGVWQQNVFAYYLSIACNHCEDPACTKVCPSGAMHKREDGFVVVNEEVCIGCRYCHMACPYGAPQYNADKGHMTKCDGCHERVAEGKKPICVESCPLRALDFGPIAELRAKHGQLAAVAPLPSAHFTRPSIVIKPNANARPCGDTTGYLANPKEV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
Unknown

Gene Ontology (GO)

4
  • 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:0046872 Binding to a metal ion.
  • 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:0045333 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
5 35 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
5 35 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
12 26 Pfam PF12800 4Fe-4S binding domain
12 26 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
73 125 FunFam G3DSA:3.30.70.20:FF:000003 Dimethyl sulfoxide reductase subunit B
6 153 CDD cd16371 DMSOR_beta_like
90 119 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
90 119 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
4 163 NCBIfam TIGR02951 dimethylsulfoxide reductase subunit B
4 163 InterPro IPR014297 Dimethylsulphoxide reductase, chain B
57 89 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
57 89 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
73 125 Gene3D G3DSA:3.30.70.20 -
3 195 SUPERFAMILY SSF54862 4Fe-4S ferredoxins
5 181 Gene3D G3DSA:3.30.70.20 -
3 190 PANTHER PTHR43177 PROTEIN NRFC
99 110 ProSitePatterns PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature.
99 110 InterPro IPR017900 4Fe-4S ferredoxin, iron-sulphur binding, conserved site
59 153 Pfam PF13247 4Fe-4S dicluster domain
59 153 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain

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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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
0.037
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.028
Likely same site as FPocket 2 1.8 Å 3 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.022
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.006
Show in viewer
Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #2
0.385
Likely same site as P2Rank 2 1.8 Å 3 shared residues 100% of smaller site
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_A0A0H3GX32
AlphaFold DB full sequence Viewing
ColabFold KP13_01159
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.

65 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 15 records from similar proteins
Structural ligands 15 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
3PH PDB via homolog Detail RCSB PDB
6MO PDB via homolog Detail RCSB PDB
AGA PDB via homolog Detail RCSB PDB
BSY 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 Q8GC87 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@@](=…
3PH RCSB PDB P11349 705.0 Da LogP 12.07 TPSA 119.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O…
6MO RCSB PDB P11349 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo+6]
AGA RCSB PDB P11349 455.5 Da LogP 1.85 TPSA 151.7 ✓ Ro5 ✓ Clean CCCCCCCC(=O)O[C@H](COC(=O)CCCC)COP(=O)([O-])OC[…
BSY RCSB PDB G8QM54 128.0 Da LogP -2.25 TPSA 60.4 ✓ Ro5 ✓ Clean O[Se](=O)[O-]
CDL RCSB PDB P0AAJ3 1464.1 Da LogP 23.31 TPSA 242.6 3 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC(…
F3S RCSB PDB P11349 295.8 Da LogP 2.59 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]2S[Fe]3[S]2[Fe]1S3
HQO RCSB PDB P0AAJ3 259.3 Da LogP 3.69 TPSA 47.2 ✓ Ro5 Alert CCCCCCCc1cc(c2ccccc2[n+]1[O-])O
MD1 RCSB PDB P11349 740.6 Da LogP -2.13 TPSA 358.0 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
MGD RCSB PDB Q7WTT9 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 Q7WTT9 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo]
O RCSB PDB Q7WTT9 18.0 Da LogP -0.82 TPSA 31.5 ✓ Ro5 ✓ Clean O
PCI RCSB PDB P11349 266.3 Da LogP 4.66 TPSA 20.2 ✓ Ro5 ✓ Clean c1(c(c(c(c(c1Cl)Cl)Cl)Cl)Cl)O
PG5 RCSB PDB Q7WTT9 178.2 Da LogP 0.31 TPSA 36.9 ✓ Ro5 ✓ Clean COCCOCCOCCOC
W RCSB PDB Q8GC87 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.