Protein target profile
KP13_01731
Ubiquinone/menaquinone biosynthesis methyltransferase ubiE
Promising target candidate with multiple supporting evidence streams.
Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.
Main supporting evidence
Risks to review
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 (%)
- 56.0 Lower values reduce human off-target concern.
- Human E-value
- 9.14e-11
- Gut microbiome similarity
- 5.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- Y
- DEG identity (%)
- 92.032 Higher values support similarity to known essential genes.
- DEG E-value
- 0.0 Smaller values mean stronger essential-gene similarity.
Localization
- Localization
- Cytoplasmic
Structure confidence
- ColabFold pLDDT
- 91.25 0-100 confidence; >70 supports local structural interpretation.
Binding-site evidence
AlphaFold DB / UniProt modelThe selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.
Cross-references
External database identifiers for this protein, its structures, ligands, and metabolic reactions.
Sequence
Sequence
Primary amino-acid sequence viewer.
MVEDSQETTHFGFQTVAKEQKADMVAHVFHSVAAKYDVMNDLMSFGIHRLWKRFTIDCSGVRRGQTVLDLAGGTGDLTAKFSRLVGETGRVMLADINDSMLKMGREKLRNIGIVGNVEYVQANAEALPFADNTFDCITISFGLRNVTDKEKALRSMYRVLKPGGRLLVLEFSKPILEPLSKAYDAYSFHILPKVGELVAKDGDSYRYLAESIRMHPDQETLKGMMQDAGFENVDYYNLTAGIVALHRGYKF
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Gene Ontology (GO)
6- GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
- GO:0008425 Catalysis of the reaction: a 2-methoxy-6-all-trans-polyprenyl-1,4-benzoquinol + S-adenosyl-L-methionine = a 6-methoxy-3-methyl-2-all-trans-polyprenyl-1,4-benzoquinol + S-adenosyl-L-homocysteine + H+.
- GO:0043770 Catalysis of the reaction: a 2-demethylmenaquinol + S-adenosyl-L-methionine = a menaquinol + H+ + S-adenosyl-L-homocysteine. Reaction substrates can have varying polyprenyl side chain length.
- GO:0009060 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
- GO:0009234 The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.
- GO:0032259 The process in which a methyl group is covalently attached to a molecule.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 36 | 51 | ProSitePatterns | PS01183 | ubiE/COQ5 methyltransferase family signature 1. |
| 36 | 51 | InterPro | IPR023576 | UbiE/COQ5 methyltransferase, conserved site |
| 27 | 233 | PANTHER | PTHR43591 | METHYLTRANSFERASE |
| 25 | 250 | NCBIfam | TIGR01934 | ubiquinone/menaquinone biosynthesis methyltransferase |
| 25 | 250 | InterPro | IPR004033 | UbiE/COQ5 methyltransferase |
| 18 | 249 | SUPERFAMILY | SSF53335 | S-adenosyl-L-methionine-dependent methyltransferases |
| 18 | 249 | InterPro | IPR029063 | S-adenosyl-L-methionine-dependent methyltransferase superfamily |
| 31 | 251 | FunFam | G3DSA:3.40.50.150:FF:000014 | Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE |
| 16 | 250 | Hamap | MF_01813 | Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE [ubiE]. |
| 16 | 250 | InterPro | IPR004033 | UbiE/COQ5 methyltransferase |
| 20 | 250 | ProSiteProfiles | PS51608 | UbiE family SAM-binding methyltransferase profile. |
| 20 | 250 | InterPro | IPR004033 | UbiE/COQ5 methyltransferase |
| 31 | 251 | Gene3D | G3DSA:3.40.50.150 | Vaccinia Virus protein VP39 |
| 31 | 251 | InterPro | IPR029063 | S-adenosyl-L-methionine-dependent methyltransferase superfamily |
| 15 | 250 | Pfam | PF01209 | ubiE/COQ5 methyltransferase family |
| 66 | 168 | CDD | cd02440 | AdoMet_MTases |
| 158 | 172 | ProSitePatterns | PS01184 | ubiE/COQ5 methyltransferase family signature 2. |
| 158 | 172 | InterPro | IPR023576 | UbiE/COQ5 methyltransferase, conserved site |
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.
How colors and pocket overlays are used
Pocket details Inspect a specific pocket, or open the full viewer
- Method
- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
Selecting a pocket opens its details and centers the viewer without clearing other active layers. Use Focus this pocket when you want to hide the rest; use Surface for the wider residue environment.
Binding pockets · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Residue sets
Binding pockets · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
All structural evidence
Structural evidence
0 + 2Experimental 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_A0A0H3GLM9
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
KP13_01731
|
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.
Structural ligand evidence is available for this target.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.
No PDB structure with a co-crystallized ligand found for this exact protein.
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.
| Ligand | Source crystal | UniProt (homolog) | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| ARS RCSB PDB | C0JV69 | 74.9 Da LogP -0.38 TPSA 0.0 | ✓ Ro5 | ✓ Clean |
[As]
|
|
| BY9 RCSB PDB | Q0H2W9 | 487.5 Da LogP 1.29 TPSA 157.0 | 1 viol. | ✓ Clean |
c1ccc2c(c1)c3c4c(c5c6ccccc6n(c5c3[nH]2)[C@H]7[C…
|
|
| DTT RCSB PDB | C0JV69 | 154.3 Da LogP -0.43 TPSA 40.5 | ✓ Ro5 | ✓ Clean |
C([C@@H]([C@H](CS)O)O)S
|
|
| MLI RCSB PDB | Q9ALM7 | 102.0 Da LogP -3.12 TPSA 80.3 | ✓ Ro5 | ✓ Clean |
C(C(=O)[O-])C(=O)[O-]
|
|
| PA0 RCSB PDB | C0JV69 | 168.0 Da LogP 0.36 TPSA 17.1 | ✓ Ro5 | ✓ Clean |
c1ccc(cc1)[As]=O
|
|
| PC RCSB PDB | Q9FR44 | 184.2 Da LogP -0.20 TPSA 66.8 | ✓ Ro5 | ✓ Clean |
C[N+](C)(C)CCOP(=O)(O)O
|
|
| RXO RCSB PDB | C0JV69 | 215.0 Da LogP -0.44 TPSA 63.4 | ✓ Ro5 | ✓ Clean |
c1cc(c(cc1[AsH2])[N+](=O)[O-])O
|
|
| TEX RCSB PDB | A0A077K7L1 | 437.6 Da LogP 4.85 TPSA 68.4 | ✓ Ro5 | Alert |
CC(C)[C@H]1C(=O)N[C@@H](Cc2c[nH]c3c2c(ccc3[C@](…
|
Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL bioactivity data found for this exact protein.
Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL hits found through similar proteins.
Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).
| Ligand | Tanimoto | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|
| ZINC2383097 ZINC | 1.000 | 437.6 Da LogP 4.85 TPSA 68.4 | ✓ Ro5 | Alert |
C=C[C@](C)(CCC=C(C)C)c1ccc2c3c(c[nH]c13)C[C@@H]…
|
| ZINC31333229 ZINC | 1.000 | 437.6 Da LogP 4.85 TPSA 68.4 | ✓ Ro5 | Alert |
C=C[C@@](C)(CCC=C(C)C)c1ccc2c3c(c[nH]c13)C[C@@H…
|
| ZINC3873176 ZINC | 1.000 | 437.6 Da LogP 4.85 TPSA 68.4 | ✓ Ro5 | Alert |
C=C[C@](C)(CCC=C(C)C)c1ccc2c3c(c[nH]c13)C[C@@H]…
|
| ZINC3873177 ZINC | 1.000 | 437.6 Da LogP 4.85 TPSA 68.4 | ✓ Ro5 | Alert |
C=C[C@](C)(CCC=C(C)C)c1ccc2c3c(c[nH]c13)C[C@H](…
|
| ZINC3873178 ZINC | 1.000 | 437.6 Da LogP 4.85 TPSA 68.4 | ✓ Ro5 | Alert |
C=C[C@](C)(CCC=C(C)C)c1ccc2c3c(c[nH]c13)C[C@H](…
|
| ZINC104949681 ZINC | 0.787 | 453.6 Da LogP 3.82 TPSA 88.6 | ✓ Ro5 | Alert |
C=C[C@](C)(CC[C@H](O)C(=C)C)c1ccc2c3c(c[nH]c13)…
|
| ZINC104949684 ZINC | 0.787 | 453.6 Da LogP 3.82 TPSA 88.6 | ✓ Ro5 | Alert |
C=C[C@](C)(CC[C@H](O)C(=C)C)c1ccc2c3c(c[nH]c13)…
|
| ZINC104949689 ZINC | 0.787 | 453.6 Da LogP 3.82 TPSA 88.6 | ✓ Ro5 | Alert |
C=C[C@](C)(CC[C@H](O)C(=C)C)c1ccc2c3c(c[nH]c13)…
|
| ZINC104949693 ZINC | 0.787 | 453.6 Da LogP 3.82 TPSA 88.6 | ✓ Ro5 | Alert |
C=C[C@](C)(CC[C@H](O)C(=C)C)c1ccc2c3c(c[nH]c13)…
|
| ZINC94568720 ZINC | 0.655 | 265.0 Da LogP 1.90 TPSA 63.4 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(I)ccc1O
|
| ZINC36377933 ZINC | 0.600 | 218.0 Da LogP 2.06 TPSA 63.4 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(Br)ccc1O
|
| ZINC167149949 ZINC | 0.586 | 457.5 Da LogP 2.67 TPSA 119.7 | ✓ Ro5 | ✓ Clean |
C[C@@H]1O[C@H](n2c3ccccc3c3c4c(c5c6ccccc6[nH]c5…
|
| ZINC248002323 ZINC | 0.586 | 457.5 Da LogP 2.67 TPSA 119.7 | ✓ Ro5 | ✓ Clean |
C[C@@H]1O[C@H](n2c3ccccc3c3c4c(c5c6ccccc6[nH]c5…
|
| ZINC248002325 ZINC | 0.586 | 457.5 Da LogP 2.67 TPSA 119.7 | ✓ Ro5 | ✓ Clean |
C[C@@H]1O[C@H](n2c3ccccc3c3c4c(c5c6ccccc6[nH]c5…
|
| ZINC38658661 ZINC | 0.586 | 457.5 Da LogP 2.67 TPSA 119.7 | ✓ Ro5 | ✓ Clean |
C[C@@H]1O[C@@H](n2c3ccccc3c3c4c(c5c6ccccc6[nH]c…
|
| ZINC83923135 ZINC | 0.586 | 457.5 Da LogP 2.67 TPSA 119.7 | ✓ Ro5 | ✓ Clean |
C[C@@H]1O[C@H](n2c3ccccc3c3c4c(c5c6ccccc6[nH]c5…
|
| ZINC1651546 ZINC | 0.581 | 304.2 Da LogP 2.15 TPSA 143.8 | ✓ Ro5 | ✓ Clean |
O=C(c1ccc(O)c([N+](=O)[O-])c1)c1ccc(O)c([N+](=O…
|
| ZINC1672250 ZINC | 0.581 | 340.3 Da LogP 1.75 TPSA 160.9 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(S(=O)(=O)c2ccc(O)c([N+](=O)[O-…
|
| ZINC1696886 ZINC | 0.581 | 290.2 Da LogP 2.51 TPSA 126.7 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(Cc2ccc(O)c([N+](=O)[O-])c2)ccc…
|
| ZINC95482938 ZINC | 0.577 | 200.1 Da LogP 0.91 TPSA 126.7 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(O)c([N+](=O)[O-])cc1O
|
| ZINC2517049 ZINC | 0.569 | 301.4 Da LogP 1.66 TPSA 68.4 | ✓ Ro5 | ✓ Clean |
CC(C)[C@H]1C(=O)N[C@H](CO)Cc2c[nH]c3cccc(c23)N1C
|
| ZINC57363 ZINC | 0.569 | 301.4 Da LogP 1.66 TPSA 68.4 | ✓ Ro5 | ✓ Clean |
CC(C)[C@@H]1C(=O)N[C@@H](CO)Cc2c[nH]c3cccc(c23)…
|
| ZINC1651909 ZINC | 0.563 | 219.2 Da LogP 0.55 TPSA 117.7 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(S(=O)(=O)O)ccc1O
|
| ZINC24718402 ZINC | 0.563 | 231.2 Da LogP 2.67 TPSA 83.6 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(-c2ccc(O)cc2)ccc1O
|
| ZINC4174041 ZINC | 0.563 | 218.2 Da LogP -0.05 TPSA 123.5 | ✓ Ro5 | ✓ Clean |
NS(=O)(=O)c1ccc(O)c([N+](=O)[O-])c1
|
| ZINC1850960 ZINC | 0.556 | 200.1 Da LogP 0.91 TPSA 126.7 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc([N+](=O)[O-])c(O)cc1O
|
| ZINC113027531 ZINC | 0.548 | 310.4 Da LogP 3.58 TPSA 55.8 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCO[P@](=O)(O)OCC[N+](C)(C)C
|
| ZINC1560408744 ZINC | 0.548 | 257.2 Da LogP -0.28 TPSA 96.2 | ✓ Ro5 | ✓ Clean |
C[N+](C)(C)CCO[P@](=O)(O)OC[C](O)CO
|
| ZINC217410460 ZINC | 0.548 | 338.4 Da LogP 4.36 TPSA 55.8 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCO[P@@](=O)(O)OCC[N+](C)(C)C
|
| ZINC3649862 ZINC | 0.548 | 296.4 Da LogP 3.19 TPSA 55.8 | ✓ Ro5 | ✓ Clean |
CCCCCCCCO[P@](=O)(O)OCC[N+](C)(C)C
|
| ZINC43562168 ZINC | 0.548 | 352.5 Da LogP 4.75 TPSA 55.8 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCO[P@@](=O)(O)OCC[N+](C)(C)C
|
| ZINC58660415 ZINC | 0.548 | 324.4 Da LogP 3.97 TPSA 55.8 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCO[P@@](=O)(O)OCC[N+](C)(C)C
|
| ZINC125976582 ZINC | 0.545 | 203.2 Da LogP 0.88 TPSA 100.7 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc([S@@](=O)O)ccc1O
|
| ZINC156016 ZINC | 0.545 | 207.1 Da LogP 2.32 TPSA 63.4 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(C(F)(F)F)ccc1O
|
| ZINC1577071 ZINC | 0.545 | 318.3 Da LogP 3.24 TPSA 126.7 | ✓ Ro5 | ✓ Clean |
CC(C)(c1ccc(O)c([N+](=O)[O-])c1)c1ccc(O)c([N+](…
|
| ZINC343430 ZINC | 0.545 | 217.2 Da LogP 0.70 TPSA 97.5 | ✓ Ro5 | ✓ Clean |
CS(=O)(=O)c1ccc(O)c([N+](=O)[O-])c1
|
| ZINC35575724 ZINC | 0.545 | 215.2 Da LogP 2.97 TPSA 63.4 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(-c2ccccc2)ccc1O
|
| ZINC1700830 ZINC | 0.541 | 294.3 Da LogP -1.70 TPSA 124.8 | ✓ Ro5 | ✓ Clean |
O=c1[nH]c(=O)n([C@@H]2O[C@@H](CO)[C@@H](O)[C@H]…
|
| ZINC4990785 ZINC | 0.541 | 294.3 Da LogP -1.70 TPSA 124.8 | ✓ Ro5 | ✓ Clean |
O=c1[nH]c(=O)n([C@H]2O[C@@H](CO)[C@@H](O)[C@H]2…
|
| ZINC4990786 ZINC | 0.541 | 294.3 Da LogP -1.70 TPSA 124.8 | ✓ Ro5 | ✓ Clean |
O=c1[nH]c(=O)n([C@H]2O[C@@H](CO)[C@@H](O)[C@@H]…
|
| ZINC4990788 ZINC | 0.541 | 294.3 Da LogP -1.70 TPSA 124.8 | ✓ Ro5 | ✓ Clean |
O=c1[nH]c(=O)n([C@@H]2O[C@@H](CO)[C@@H](O)[C@@H…
|
| ZINC96031232 ZINC | 0.531 | 353.5 Da LogP 3.30 TPSA 81.8 | ✓ Ro5 | ✓ Clean |
C[N+](C)(C)CCO[P@@](=O)(O)OCCCCCCCCCCCN
|
| ZINC37246177 ZINC | 0.529 | 371.1 Da LogP 4.11 TPSA 126.7 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(C(=C(Cl)Cl)c2ccc(O)c([N+](=O)[…
|
| ZINC34240224 ZINC | 0.519 | 200.1 Da LogP 0.91 TPSA 126.7 | ✓ Ro5 | Alert |
O=[N+]([O-])c1cc(O)c(O)cc1[N+](=O)[O-]
|
| ZINC21303651 ZINC | 0.516 | 234.0 Da LogP 1.77 TPSA 83.6 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(Br)c(O)cc1O
|
| ZINC1532714 ZINC | 0.515 | 258.2 Da LogP -0.82 TPSA 96.2 | ✓ Ro5 | ✓ Clean |
C[N+](C)(C)CCO[P@@](=O)(O)OC[C@H](O)CO
|
| ZINC1842903 ZINC | 0.515 | 258.2 Da LogP -0.82 TPSA 96.2 | ✓ Ro5 | ✓ Clean |
C[N+](C)(C)CCO[P@](=O)(O)OC[C@@H](O)CO
|
| ZINC1507325 ZINC | 0.514 | 271.2 Da LogP 1.59 TPSA 97.5 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(S(=O)(=O)C(F)(F)F)ccc1O
|
| ZINC21985628 ZINC | 0.514 | 426.2 Da LogP 4.32 TPSA 126.7 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(C(c2ccc(O)c([N+](=O)[O-])c2)(C…
|
| ZINC2562578 ZINC | 0.514 | 231.2 Da LogP 1.09 TPSA 97.5 | ✓ Ro5 | ✓ Clean |
CCS(=O)(=O)c1ccc(O)c([N+](=O)[O-])c1
|
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.