NP-MRD: Showing NP-Card for Hymeglusin (NP0351377)

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Record Information

Version

2.0

Created at

2025-07-30 14:45:30 UTC

Updated at

2025-08-01 00:01:40 UTC

NP-MRD ID

NP0351377

Natural Product DOI

https://doi.org/10.57994/4418

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Hymeglusin

Description

Hymeglusin, also known as antibiotic 1233A, belongs to the class of organic compounds known as long-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 13 and 21 carbon atoms. Hymeglusin was first documented in 2024 (PMID: 39035915). Based on a literature review a small amount of articles have been published on Hymeglusin (PMID: 40684465) (PMID: 40635350) (PMID: 40631324) (PMID: 38994525).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 02032307562D          

 23 23  0  0  1  0            999 V2000
    3.3383   -0.1428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3383   -0.9678    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6238   -1.3803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9093   -0.9678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1948   -1.3803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4804   -0.9678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2341   -1.3803    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4476   -2.1771    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2445   -1.9636    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9590   -2.3761    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0310   -1.1667    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0351   -2.8916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4476   -3.6061    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0527   -1.3803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7672   -0.9678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4817   -1.3803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1961   -0.9678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9106   -1.3803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6251   -0.9678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6251   -0.1428    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.3395   -1.3803    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1961   -0.1428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7672   -0.1428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  7  6  1  6  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  7 11  1  0  0  0  0
  8 12  1  1  0  0  0
 12 13  1  0  0  0  0
  2 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
 17 22  1  0  0  0  0
 15 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0351377

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](CCCC[C@H]1OC(=O)[C@@H]1CO)C\C(C)=C\C(\C)=C\C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C18H28O5/c1-12(8-13(2)9-14(3)10-17(20)21)6-4-5-7-16-15(11-19)18(22)23-16/h9-10,12,15-16,19H,4-8,11H2,1-3H3,(H,20,21)/b13-9+,14-10+/t12-,15-,16-/m1/s1

> <INCHI_KEY>
ODCZJZWSXPVLAW-KXCGKLMDSA-N

> <FORMULA>
C18H28O5

> <MOLECULAR_WEIGHT>
324.417

> <EXACT_MASS>
324.193674002

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
51

> <JCHEM_AVERAGE_POLARIZABILITY>
36.445885439490795

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2E,4E,7R)-11-[(2R,3R)-3-(hydroxymethyl)-4-oxooxetan-2-yl]-3,5,7-trimethylundeca-2,4-dienoic acid

> <JCHEM_LOGP>
3.1527223346666675

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.14894216769964

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.8613584043305265

> <JCHEM_PKA_STRONGEST_BASIC>
-2.733652695857973

> <JCHEM_POLAR_SURFACE_AREA>
83.83

> <JCHEM_REFRACTIVITY>
89.24199999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2E,4E,7R)-11-[(2R,3R)-3-(hydroxymethyl)-4-oxooxetan-2-yl]-3,5,7-trimethylundeca-2,4-dienoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-FEB-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-FEB-23         0                                  
HETATM    1  C   UNK     0       6.231  -0.266   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.231  -1.806   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.898  -2.576   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.564  -1.806   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.230  -2.576   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.897  -1.806   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.437  -2.576   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.836  -4.064   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.323  -3.665   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -3.657  -4.435   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -1.925  -2.178   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -0.066  -5.398   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -0.836  -6.731   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       7.565  -2.576   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.899  -1.806   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.232  -2.576   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      11.566  -1.806   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      12.900  -2.576   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      14.233  -1.806   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      14.233  -0.266   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      15.567  -2.576   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      11.566  -0.266   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.899  -0.266   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   14                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   11                                                  
CONECT    8    7    9   12                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9    7                                                       
CONECT   12    8   13                                                       
CONECT   13   12                                                            
CONECT   14    2   15                                                       
CONECT   15   14   16   23                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   22                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19                                                            
CONECT   22   17                                                            
CONECT   23   15                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   46    0
END

View in JSmol

Synonyms

Value	Source
Antibiotic 1233a sodium	HMDB
11-(3-(Hydroxymethyl)-4-oxo-2-oxytanyl)-3,5,7-trimethyl-2,4-undecadienenoic acid	HMDB
3,5,7-Trimethyl-12-hydroxy-13-hydroxymethyl-2,4-tetradecadiendioic acid 12,14-lactone	HMDB
Antibiotic 1233a	HMDB
Antibiotic 1233a calcium	HMDB
11-(3'-(Hydroxymethyl)-4'-oxo-2'-oxetanyl)-3,5,7-trimethyl-2,4-undecadienoic acid	HMDB
Antibiotic 1233a potassium	HMDB

Chemical Formula

C₁₈H₂₈O₅

Average Mass

324.4170 Da

Monoisotopic Mass

324.19367 Da

IUPAC Name

(2E,4E,7R)-11-[(2R,3R)-3-(hydroxymethyl)-4-oxooxetan-2-yl]-3,5,7-trimethylundeca-2,4-dienoic acid

Traditional Name

(2E,4E,7R)-11-[(2R,3R)-3-(hydroxymethyl)-4-oxooxetan-2-yl]-3,5,7-trimethylundeca-2,4-dienoic acid

CAS Registry Number

Not Available

SMILES

C[C@H](CCCC[C@H]1OC(=O)[C@@H]1CO)C\C(C)=C\C(\C)=C\C(O)=O

InChI Identifier

InChI=1S/C18H28O5/c1-12(8-13(2)9-14(3)10-17(20)21)6-4-5-7-16-15(11-19)18(22)23-16/h9-10,12,15-16,19H,4-8,11H2,1-3H3,(H,20,21)/b13-9+,14-10+/t12-,15-,16-/m1/s1

InChI Key

ODCZJZWSXPVLAW-KXCGKLMDSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CD3OD, experimental)	gabi.almeida@usp.br	University of São Paulo	Gabriela de Oliveira Almeida	2025-07-30	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Fusarium falciforme		Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as long-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 13 and 21 carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Long-chain fatty acids

Alternative Parents

Substituents

Long-chain fatty acid
Branched fatty acid
Heterocyclic fatty acid
Hydroxy fatty acid
Methyl-branched fatty acid
Dicarboxylic acid or derivatives
Unsaturated fatty acid
Beta_propiolactone
Carboxylic acid ester
Lactone
Oxetane
Organoheterocyclic compound
Oxacycle
Carboxylic acid
Carboxylic acid derivative
Hydrocarbon derivative
Alcohol
Carbonyl group
Organic oxide
Primary alcohol
Organooxygen compound
Organic oxygen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	3.15	ChemAxon
pKa (Strongest Acidic)	4.86	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	83.83 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	89.24 m³·mol⁻¹	ChemAxon
Polarizability	36.45 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0341330

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

4945132

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6440895

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

de Oliveira Almeida G, Mazucato VS, Tonani L, von Zeska Kress MR, Barbosa G, Krogh R, Andricopulo AD, Gomes Ferreira LL, Vieira PC: Exploring Bioactive Metabolites From Fusarium falciforme and Aspergillus terreus Isolated From Protease-Rich Fruits: Antifungal, Antitrypanosomal, and Enzymatic Inhibitory Activities. Chem Biodivers. 2025 Jul 20:e00673. doi: 10.1002/cbdv.202500673. [PubMed:40684465 ]
Hirokawa M, Ozaki T, Tsukada K, Sugawara A, Morishita Y, Asai T: Ketosynthase Domain Catalyzes beta-Lactonization in the Biosynthesis of the HMG-CoA Synthase Inhibitor Hymeglusin. J Am Chem Soc. 2025 Jul 23;147(29):25136-25141. doi: 10.1021/jacs.5c07060. Epub 2025 Jul 10. [PubMed:40635350 ]
Yi SA, Sun L, Rao Y, Ordureau A, Lewis JS, An H: Activity-based probes and chemical proteomics uncover the biological impact of targeting HMGCS1. bioRxiv [Preprint]. 2025 Jul 1:2025.05.21.655359. doi: 10.1101/2025.05.21.655359. [PubMed:40631324 ]
Chemutai Sum W, Ebada SS, Wang H, Kellner H, Stadler M: Protoilludene and Alkenoic Acid Derivatives from the European Polypore Fomitiporia hartigii. ACS Omega. 2024 Jul 4;9(28):31006-31010. doi: 10.1021/acsomega.4c04287. eCollection 2024 Jul 16. [PubMed:39035915 ]
Zhou C, Li J, Sun X, Zhao L, Zhan H, Liang H, Fang P, Zhang T, He Q, Du J, Zeng H: Targeting HMGCS1 restores chemotherapy sensitivity in acute myeloid leukemia. Blood Sci. 2024 Jul 10;6(3):e00192. doi: 10.1097/BS9.0000000000000192. eCollection 2024 Jul. [PubMed:38994525 ]
DOI: 10.1002/cbdv.202500673
PMID: 40684465

Showing NP-Card for Hymeglusin (NP0351377)

MOL for NP0351377 (Hymeglusin)

3D MOL for NP0351377 (Hymeglusin)

3D SDF for NP0351377 (Hymeglusin)

3D-SDF for NP0351377 (Hymeglusin)

PDB for NP0351377 (Hymeglusin)

3D PDB for NP0351377 (Hymeglusin)

SMILES for NP0351377 (Hymeglusin)

INCHI for NP0351377 (Hymeglusin)

Structure for NP0351377 (Hymeglusin)

3D Structure for NP0351377 (Hymeglusin)