NP-MRD: Showing NP-Card for MDN-0060 (NP0341942)

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Record Information

Version

2.0

Created at

2024-11-06 14:52:36 UTC

Updated at

2026-02-06 08:00:46 UTC

NP-MRD ID

NP0341942

Natural Product DOI

https://doi.org/10.57994/3432

Secondary Accession Numbers

None

Natural Product Identification

Common Name

MDN-0060

Description

MDN-0060 was first documented in 2025 (PMID: 39893688).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 02032315032D          

 28 29  0  0  1  0            999 V2000
   -0.6039   -3.9039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105   -3.4914    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1105   -2.6664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -2.2539    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8250   -1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -2.1434    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -0.8250   -2.8579    0.0000 C   0  5  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.6039    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.8250    0.2211    0.0000 C   0  5  0  0  0  0  0  0  0  0  0  0
    1.6500   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -1.8414    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -2.6664    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2539   -2.2539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684   -2.6664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684   -3.4914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -3.4914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -3.9039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  4  3  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  3  0  0  0  0
  6  9  2  0  0  0  0
  5 10  1  6  0  0  0
 10 11  3  0  0  0  0
  5 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  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  1  0  0  0  0
 16 19  1  0  0  0  0
 19 20  2  0  0  0  0
 13 20  1  0  0  0  0
  4 21  1  1  0  0  0
  4 22  1  0  0  0  0
 22 23  1  1  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  2  0  0  0  0
 22 27  1  0  0  0  0
 27 28  2  0  0  0  0
  2 28  1  0  0  0  0
M  CHG  4   7   1   8  -1  10   1  11  -1
M  END


  Mrv2104 02032315032D          

 28 29  0  0  1  0            999 V2000
   -0.6039   -3.9039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105   -3.4914    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1105   -2.6664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -2.2539    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8250   -1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -2.1434    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -0.8250   -2.8579    0.0000 C   0  5  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.6039    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.8250    0.2211    0.0000 C   0  5  0  0  0  0  0  0  0  0  0  0
    1.6500   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -1.8414    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -2.6664    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2539   -2.2539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684   -2.6664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684   -3.4914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -3.4914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -3.9039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  4  3  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  3  0  0  0  0
  6  9  2  0  0  0  0
  5 10  1  6  0  0  0
 10 11  3  0  0  0  0
  5 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  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  1  0  0  0  0
 16 19  1  0  0  0  0
 19 20  2  0  0  0  0
 13 20  1  0  0  0  0
  4 21  1  1  0  0  0
  4 22  1  0  0  0  0
 22 23  1  1  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  2  0  0  0  0
 22 27  1  0  0  0  0
 27 28  2  0  0  0  0
  2 28  1  0  0  0  0
M  CHG  4   7   1   8  -1  10   1  11  -1
M  END
> <DATABASE_ID>
NP0341942

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]1(C[C@@H](O)C=C[C@@H]1OC(C)=O)[C@@](CC1=CC=C(OC)C=C1)([N+]#[C-])C(=C)[N+]#[C-]

> <INCHI_IDENTIFIER>
InChI=1S/C21H22N2O4/c1-14(22-3)21(23-4,13-16-6-9-18(26-5)10-7-16)19-12-17(25)8-11-20(19)27-15(2)24/h6-11,17,19-20,25H,1,12-13H2,2,5H3/t17-,19-,20-,21-/m0/s1

> <INCHI_KEY>
JXHBZWLNYQFXEY-VMXMFDLUSA-N

> <FORMULA>
C21H22N2O4

> <MOLECULAR_WEIGHT>
366.417

> <EXACT_MASS>
366.157957196

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
49

> <JCHEM_AVERAGE_POLARIZABILITY>
38.299142476695394

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,4R,6R)-6-[(2R)-2,3-diisocyano-1-(4-methoxyphenyl)but-3-en-2-yl]-4-hydroxycyclohex-2-en-1-yl acetate

> <JCHEM_LOGP>
-2.2557166724185587

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
15.941477262057699

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.82483731903334

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8591739604156166

> <JCHEM_POLAR_SURFACE_AREA>
64.47999999999999

> <JCHEM_REFRACTIVITY>
120.1528

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,4R,6R)-6-[(2R)-2,3-diisocyano-1-(4-methoxyphenyl)but-3-en-2-yl]-4-hydroxycyclohex-2-en-1-yl acetate

> <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  O   UNK     0      -1.127  -7.287   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.206  -6.517   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.206  -4.977   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.540  -4.207   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.540  -2.667   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000  -2.667   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -0.770  -4.001   0.000  0.00  0.00           N+1
HETATM    8  C   UNK     0      -1.540  -5.335   0.000  0.00  0.00           C-1
HETATM    9  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       1.540  -1.127   0.000  0.00  0.00           N+1
HETATM   11  C   UNK     0       1.540   0.413   0.000  0.00  0.00           C-1
HETATM   12  C   UNK     0       3.080  -2.667   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.080   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.850   1.334   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.390   1.334   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       6.160   2.667   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       7.700   2.667   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.160   0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.390  -1.334   0.000  0.00  0.00           C+0
HETATM   21  H   UNK     0       2.874  -3.437   0.000  0.00  0.00           H+0
HETATM   22  C   UNK     0       2.874  -4.977   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       4.207  -4.207   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       5.541  -4.977   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.875  -4.207   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       5.541  -6.517   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       2.874  -6.517   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.540  -7.287   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   28                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   21   22                                             
CONECT    5    4    6   10   12                                             
CONECT    6    5    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7                                                            
CONECT    9    6                                                            
CONECT   10    5   11                                                       
CONECT   11   10                                                            
CONECT   12    5   13                                                       
CONECT   13   12   14   20                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   19                                                  
CONECT   17   16   18                                                       
CONECT   18   17                                                            
CONECT   19   16   20                                                       
CONECT   20   19   13                                                       
CONECT   21    4                                                            
CONECT   22    4   23   27                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24                                                            
CONECT   27   22   28                                                       
CONECT   28   27    2                                                       
MASTER        0    0    0    0    0    0    0    0   28    0   58    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₁H₂₂N₂O₄

Average Mass

366.4170 Da

Monoisotopic Mass

366.15796 Da

IUPAC Name

(1S,4R,6R)-6-[(2R)-2,3-diisocyano-1-(4-methoxyphenyl)but-3-en-2-yl]-4-hydroxycyclohex-2-en-1-yl acetate

Traditional Name

(1S,4R,6R)-6-[(2R)-2,3-diisocyano-1-(4-methoxyphenyl)but-3-en-2-yl]-4-hydroxycyclohex-2-en-1-yl acetate

CAS Registry Number

Not Available

SMILES

[H][C@@]1(C[C@@H](O)C=C[C@@H]1OC(C)=O)[C@@](CC1=CC=C(OC)C=C1)([N+]#[C-])C(=C)[N+]#[C-]

InChI Identifier

InChI=1S/C21H22N2O4/c1-14(22-3)21(23-4,13-16-6-9-18(26-5)10-7-16)19-12-17(25)8-11-20(19)27-15(2)24/h6-11,17,19-20,25H,1,12-13H2,2,5H3/t17-,19-,20-,21-/m0/s1

InChI Key

JXHBZWLNYQFXEY-VMXMFDLUSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	[email protected]	Not Available	Not Available	2024-11-06	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	[email protected]	Not Available	Not Available	2024-11-06	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	[email protected]	Not Available	Not Available	2024-11-06	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CD3OD, experimental)	[email protected]	Not Available	Not Available	2024-11-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, CD3OD, experimental)	[email protected]	Not Available	Not Available	2024-11-06	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 500.0, Methanol-d4, simulated)	[email protected]	Not Available	Not Available	2026-02-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 125.0, Methanol-d4, simulated)	[email protected]	Not Available	Not Available	2026-02-06	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Ophiosphaerella korrae		Not Available
Ophiosphaerella korrae		Not Available

Chemical Taxonomy

Classification

Not classified

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	-2.3	ChemAxon
pKa (Strongest Acidic)	14.82	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	64.48 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	120.15 m³·mol⁻¹	ChemAxon
Polarizability	38.3 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Perez-Victoria I, El Aouad N, Gonzalez-Menendez V, de La Cruz M, Fernandez LL, Martin J, Tormo JR, Genta-Jouve G, Thomas OP, Vicente F, Bills GF, Genilloud O, Reyes F: MDN-0057 to MDN-0060, a Family of Broad-Spectrum Antibiotics against Gram-Negative Pathogens Produced by Ophiosphaerella korrae. J Nat Prod. 2025 Feb 28;88(2):469-476. doi: 10.1021/acs.jnatprod.4c01289. Epub 2025 Feb 2. [PubMed:39893688 ]
DOI: 10.1021/acs.jnatprod.4c01289
PMID: 39893688

Showing NP-Card for MDN-0060 (NP0341942)

MOL for NP0341942 (MDN-0060)

3D MOL for NP0341942 (MDN-0060)

3D SDF for NP0341942 (MDN-0060)

3D-SDF for NP0341942 (MDN-0060)

PDB for NP0341942 (MDN-0060)

3D PDB for NP0341942 (MDN-0060)

SMILES for NP0341942 (MDN-0060)

INCHI for NP0341942 (MDN-0060)

Structure for NP0341942 (MDN-0060)

3D Structure for NP0341942 (MDN-0060)