NP-MRD: Showing NP-Card for 6-hydroxy-4-[(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4z,6e,10e)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]-4,5-dihydro-3h-pyridin-2-one (NP0267189)

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Record Information

Version

2.0

Created at

2022-09-08 11:53:17 UTC

Updated at

2022-09-08 11:53:17 UTC

NP-MRD ID

NP0267189

Secondary Accession Numbers

None

Natural Product Identification

Common Name

6-hydroxy-4-[(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4z,6e,10e)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]-4,5-dihydro-3h-pyridin-2-one

Description

Lactimidomycin belongs to the class of organic compounds known as macrolides and analogues. These are organic compounds containing a lactone ring of at least twelve members. 6-hydroxy-4-[(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4z,6e,10e)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]-4,5-dihydro-3h-pyridin-2-one is found in Streptomyces amphibiosporus. 6-hydroxy-4-[(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4z,6e,10e)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]-4,5-dihydro-3h-pyridin-2-one was first documented in 2020 (PMID: 33145015). Based on a literature review a small amount of articles have been published on Lactimidomycin (PMID: 35491906) (PMID: 34769510) (PMID: 33458709).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309082213532D          

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M  END

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  Mrv1652309082213532D          

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M  END
> <DATABASE_ID>
NP0267189

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H](\C=C(/C)[C@@H]1OC(=O)\C=C\CC\C=C\C=C/[C@@H]1C)C(=O)C[C@H](O)CC1CC(O)=NC(=O)C1

> <INCHI_IDENTIFIER>
InChI=1S/C26H35NO6/c1-17-10-8-6-4-5-7-9-11-25(32)33-26(17)19(3)12-18(2)22(29)16-21(28)13-20-14-23(30)27-24(31)15-20/h4,6,8-12,17-18,20-21,26,28H,5,7,13-16H2,1-3H3,(H,27,30,31)/b6-4+,10-8-,11-9+,19-12+/t17-,18-,21+,26+/m0/s1

> <INCHI_KEY>
OYOKHBHOTQDIPM-BRHOHSSQSA-N

> <FORMULA>
C26H35NO6

> <MOLECULAR_WEIGHT>
457.567

> <EXACT_MASS>
457.246437851

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
49.64688862983674

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
6-hydroxy-4-[(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4Z,6E,10E)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]-2,3,4,5-tetrahydropyridin-2-one

> <JCHEM_LOGP>
3.663386039333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.8637385380142

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.4113820678782747

> <JCHEM_PKA_STRONGEST_BASIC>
-2.766620559303812

> <JCHEM_POLAR_SURFACE_AREA>
113.25999999999999

> <JCHEM_REFRACTIVITY>
129.5865

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
6-hydroxy-4-[(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4Z,6E,10E)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]-4,5-dihydro-3H-pyridin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.335  -1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.667  -1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.334  -3.850   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -0.000  -1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.334  -3.850   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       2.667  -1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335  -1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       8.002  -1.540   0.000  0.00  0.00           O+0
HETATM   16  N   UNK     0       6.668  -3.850   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       5.335  -6.160   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       4.001  -3.850   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0     -10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0     -10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -8.002   0.000   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -6.042   0.637   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   20                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   19                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   12                                                       
CONECT   20    2   21   32                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   20   33                                                  
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   68    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₃₅NO₆

Average Mass

457.5670 Da

Monoisotopic Mass

457.24644 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

C[C@@H](\C=C(/C)[C@@H]1OC(=O)\C=C\CC\C=C\C=C/[C@@H]1C)C(=O)C[C@H](O)CC1CC(O)=NC(=O)C1

InChI Identifier

InChI=1S/C26H35NO6/c1-17-10-8-6-4-5-7-9-11-25(32)33-26(17)19(3)12-18(2)22(29)16-21(28)13-20-14-23(30)27-24(31)15-20/h4,6,8-12,17-18,20-21,26,28H,5,7,13-16H2,1-3H3,(H,27,30,31)/b6-4+,10-8-,11-9+,19-12+/t17-,18-,21+,26+/m0/s1

InChI Key

OYOKHBHOTQDIPM-BRHOHSSQSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces amphibiosporus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as macrolides and analogues. These are organic compounds containing a lactone ring of at least twelve members.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Macrolides and analogues

Sub Class

Not Available

Direct Parent

Macrolides and analogues

Alternative Parents

Substituents

Macrolide
Piperidinedione
Delta-lactam
Piperidinone
Beta-hydroxy ketone
Piperidine
Carboxylic acid imide
Dicarboximide
Carboxylic acid imide, n-unsubstituted
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Secondary alcohol
Carboxylic acid ester
Ketone
Lactam
Lactone
Organoheterocyclic compound
Carboxylic acid derivative
Oxacycle
Azacycle
Monocarboxylic acid or derivatives
Organic oxygen compound
Alcohol
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Organic oxide
Carbonyl group
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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00016752

Chemspider ID

9844457

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Lactimidomycin

METLIN ID

Not Available

PubChem Compound

11669726

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Singh S, Florez H: Bioinformatic study to discover natural molecules with activity against COVID-19. F1000Res. 2020 Oct 6;9:1203. doi: 10.12688/f1000research.26731.1. eCollection 2020. [PubMed:33145015 ]
Guzikowski AR, Harvey AT, Zhang J, Zhu S, Begovich K, Cohn MH, Wilhelm JE, Zid BM: Differential translation elongation directs protein synthesis in response to acute glucose deprivation in yeast. RNA Biol. 2022;19(1):636-649. doi: 10.1080/15476286.2022.2065784. Epub 2021 Dec 31. [PubMed:35491906 ]
Dang TT, Back SH: Translation Inhibitors Activate Autophagy Master Regulators TFEB and TFE3. Int J Mol Sci. 2021 Nov 8;22(21):12083. doi: 10.3390/ijms222112083. [PubMed:34769510 ]
Hollerer I, Powers EN, Brar GA: Global mapping of translation initiation sites by TIS profiling in budding yeast. STAR Protoc. 2020 Dec 30;2(1):100250. doi: 10.1016/j.xpro.2020.100250. eCollection 2021 Mar 19. [PubMed:33458709 ]
LOTUS database [Link]

Showing NP-Card for 6-hydroxy-4-[(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4z,6e,10e)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]-4,5-dihydro-3h-pyridin-2-one (NP0267189)

MOL for NP0267189 (6-hydroxy-4-[(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4z,6e,10e)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]-4,5-dihydro-3h-pyridin-2-one)

3D MOL for NP0267189 (6-hydroxy-4-[(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4z,6e,10e)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]-4,5-dihydro-3h-pyridin-2-one)

3D SDF for NP0267189 (6-hydroxy-4-[(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4z,6e,10e)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]-4,5-dihydro-3h-pyridin-2-one)

3D-SDF for NP0267189 (6-hydroxy-4-[(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4z,6e,10e)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]-4,5-dihydro-3h-pyridin-2-one)

PDB for NP0267189 (6-hydroxy-4-[(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4z,6e,10e)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]-4,5-dihydro-3h-pyridin-2-one)

3D PDB for NP0267189 (6-hydroxy-4-[(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4z,6e,10e)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]-4,5-dihydro-3h-pyridin-2-one)

SMILES for NP0267189 (6-hydroxy-4-[(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4z,6e,10e)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]-4,5-dihydro-3h-pyridin-2-one)

INCHI for NP0267189 (6-hydroxy-4-[(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4z,6e,10e)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]-4,5-dihydro-3h-pyridin-2-one)

Structure for NP0267189 (6-hydroxy-4-[(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4z,6e,10e)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]-4,5-dihydro-3h-pyridin-2-one)

3D Structure for NP0267189 (6-hydroxy-4-[(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4z,6e,10e)-3-methyl-12-oxo-1-oxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl]-4,5-dihydro-3h-pyridin-2-one)