NP-MRD: Showing NP-Card for (1r,5s)-3-hydroxy-1-(1-hydroxy-2-methylpropyl)-4-methyl-6-oxa-2-azabicyclo[3.2.0]hept-2-en-7-one (NP0210687)

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Record Information

Version

2.0

Created at

2022-09-05 08:37:17 UTC

Updated at

2022-09-05 08:37:17 UTC

NP-MRD ID

NP0210687

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,5s)-3-hydroxy-1-(1-hydroxy-2-methylpropyl)-4-methyl-6-oxa-2-azabicyclo[3.2.0]hept-2-en-7-one

Description

Omuralide belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. (1r,5s)-3-hydroxy-1-(1-hydroxy-2-methylpropyl)-4-methyl-6-oxa-2-azabicyclo[3.2.0]hept-2-en-7-one is found in Salinispora tropica. (1r,5s)-3-hydroxy-1-(1-hydroxy-2-methylpropyl)-4-methyl-6-oxa-2-azabicyclo[3.2.0]hept-2-en-7-one was first documented in 2014 (PMID: 25436151). Based on a literature review a small amount of articles have been published on Omuralide (PMID: 35765420) (PMID: 32469026) (PMID: 30011218) (PMID: 24285701).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 30 31  0  0  0  0  0  0  0  0999 V2000
   -2.2345    1.2825    0.6248 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1511    0.1152   -0.2884 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1314   -1.1538    0.5331 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0867    0.1619   -1.3181 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3085    1.2990   -2.1363 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3091    0.2208   -0.8801 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7923    1.3106   -0.1295 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4845    0.9805    0.8948 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0840    1.8922    1.8130 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5578   -0.4894    0.9674 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9853   -0.9814    1.1248 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0062   -0.9648   -0.3398 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0026   -0.9192   -1.3658 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2206   -0.0199   -2.0608 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1900    0.4730   -3.2160 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2698    1.2699    1.0752 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5531    1.1881    1.5063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1486    2.2619    0.1311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1426    0.0824   -0.8371 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9250   -2.0134   -0.1390 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1777   -1.3320    0.9118 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4267   -1.1425    1.3612 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2207   -0.7048   -1.9988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1369    1.0756   -2.6425 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9287    2.3333    1.4826 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9100   -0.8873    1.7909 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9783   -1.9134    1.7119 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6287   -0.2657    1.6412 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3728   -1.2316    0.1029 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4626   -1.9276   -0.3208 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  1
  7  8  2  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 12  6  1  0
 14  6  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  2 19  1  0
  3 20  1  0
  3 21  1  0
  3 22  1  0
  4 23  1  6
  5 24  1  0
  9 25  1  0
 10 26  1  1
 11 27  1  0
 11 28  1  0
 11 29  1  0
 12 30  1  1
M  END


  Mrv1652309052210372D          

 15 16  0  0  1  0            999 V2000
    2.1563    2.3977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2854    1.5829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0556    1.2872    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6442    1.0637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8740    1.3593    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7733    0.2488    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5579    0.5038    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0428   -0.1637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8678   -0.1637    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5579   -0.8311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8129   -1.6157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7733   -0.5762    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9483   -0.5762    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9483    0.2488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3649    0.8322    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  6  4  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
  6 12  1  0  0  0  0
 12 13  1  6  0  0  0
 13 14  1  0  0  0  0
  6 14  1  0  0  0  0
 14 15  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0210687

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)C(O)[C@@]12N=C(O)C(C)[C@@H]1OC2=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H15NO4/c1-4(2)6(12)10-7(15-9(10)14)5(3)8(13)11-10/h4-7,12H,1-3H3,(H,11,13)/t5?,6?,7-,10+/m0/s1

> <INCHI_KEY>
FWPWHHUJACGNMZ-OECXWRGYSA-N

> <FORMULA>
C10H15NO4

> <MOLECULAR_WEIGHT>
213.233

> <EXACT_MASS>
213.100107967

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
21.29817237237897

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,5S)-3-hydroxy-1-(1-hydroxy-2-methylpropyl)-4-methyl-6-oxa-2-azabicyclo[3.2.0]hept-2-en-7-one

> <JCHEM_LOGP>
0.9083218460000002

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.841775417287877

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.958908209112397

> <JCHEM_PKA_STRONGEST_BASIC>
-1.1456467541582391

> <JCHEM_POLAR_SURFACE_AREA>
79.12

> <JCHEM_REFRACTIVITY>
50.5707

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,5S)-3-hydroxy-1-(1-hydroxy-2-methylpropyl)-4-methyl-6-oxa-2-azabicyclo[3.2.0]hept-2-en-7-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0       4.025   4.476   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.266   2.955   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.704   2.403   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.069   1.986   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.632   2.537   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       3.310   0.464   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       4.775   0.940   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       5.680  -0.306   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       7.220  -0.306   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       4.775  -1.551   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.251  -3.016   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.310  -1.076   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.770  -1.076   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       1.770   0.464   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       0.681   1.553   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   12   14                                             
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    6   13                                                  
CONECT   13   12   14                                                       
CONECT   14   13    6   15                                                  
CONECT   15   14                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₁₅NO₄

Average Mass

213.2330 Da

Monoisotopic Mass

213.10011 Da

IUPAC Name

(1R,5S)-3-hydroxy-1-(1-hydroxy-2-methylpropyl)-4-methyl-6-oxa-2-azabicyclo[3.2.0]hept-2-en-7-one

Traditional Name

(1R,5S)-3-hydroxy-1-(1-hydroxy-2-methylpropyl)-4-methyl-6-oxa-2-azabicyclo[3.2.0]hept-2-en-7-one

CAS Registry Number

Not Available

SMILES

CC(C)C(O)[C@@]12N=C(O)C(C)[C@@H]1OC2=O

InChI Identifier

InChI=1S/C10H15NO4/c1-4(2)6(12)10-7(15-9(10)14)5(3)8(13)11-10/h4-7,12H,1-3H3,(H,11,13)/t5?,6?,7-,10+/m0/s1

InChI Key

FWPWHHUJACGNMZ-OECXWRGYSA-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
Salinispora tropica	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
Oxoproline
Para-oxazepine
Pyrrolidone
2-pyrrolidone
Beta_propiolactone
Pyrrolidine
Carboxamide group
Carboxylic acid ester
Lactam
Lactone
Oxetane
Secondary alcohol
Secondary carboxylic acid amide
Monocarboxylic acid or derivatives
Oxacycle
Azacycle
Organoheterocyclic compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Alcohol
Organic oxide
Hydrocarbon derivative
Carbonyl group
Organic nitrogen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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	0.91	ChemAxon
pKa (Strongest Acidic)	4.96	ChemAxon
pKa (Strongest Basic)	-1.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	79.12 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	50.57 m³·mol⁻¹	ChemAxon
Polarizability	21.3 Å³	ChemAxon
Number of Rings	2	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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00047327

Chemspider ID

78434008

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

91746126

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Beng TK, Rodriguez MJ, Borg C: Stereocontrolled access to delta-lactone-fused-gamma-lactams bearing angular benzylic quaternary stereocenters. RSC Adv. 2022 Jun 14;12(27):17617-17620. doi: 10.1039/d2ra02167f. eCollection 2022 Jun 7. [PubMed:35765420 ]
Li F, Jager V: Synthesis of proteasome inhibitor 6-deoxy-omuralide and its enantiomer using stereoselective alkylation of substituted proline ester. Org Biomol Chem. 2020 May 29. doi: 10.1039/d0ob01053g. [PubMed:32469026 ]
Rulliere P, Cannillo A, Grisel J, Cividino P, Sebastien Carret, Poisson JF: Total Synthesis of Proteasome Inhibitor (-)-Omuralide through Asymmetric Ketene [2 + 2]-Cycloaddition. Org Lett. 2018 Aug 3;20(15):4558-4561. doi: 10.1021/acs.orglett.8b01851. Epub 2018 Jul 16. [PubMed:30011218 ]
Nayak S, Fiaschi M, King D, Tabakin ER, Wood L, Hunt DA: Development of Small Molecular Proteasome Inhibitors Using a Caenorhabditis elegans Screen. Int J Med Chem. 2014;2014:237286. doi: 10.1155/2014/237286. Epub 2014 Nov 11. [PubMed:25436151 ]
List A, Zeiler E, Gallastegui N, Rusch M, Hedberg C, Sieber SA, Groll M: Omuralide and vibralactone: differences in the proteasome- beta-lactone-gamma-lactam binding scaffold alter target preferences. Angew Chem Int Ed Engl. 2014 Jan 7;53(2):571-4. doi: 10.1002/anie.201308567. Epub 2013 Nov 28. [PubMed:24285701 ]
LOTUS database [Link]

Showing NP-Card for (1r,5s)-3-hydroxy-1-(1-hydroxy-2-methylpropyl)-4-methyl-6-oxa-2-azabicyclo[3.2.0]hept-2-en-7-one (NP0210687)

MOL for NP0210687 ((1r,5s)-3-hydroxy-1-(1-hydroxy-2-methylpropyl)-4-methyl-6-oxa-2-azabicyclo[3.2.0]hept-2-en-7-one)

3D MOL for NP0210687 ((1r,5s)-3-hydroxy-1-(1-hydroxy-2-methylpropyl)-4-methyl-6-oxa-2-azabicyclo[3.2.0]hept-2-en-7-one)

3D SDF for NP0210687 ((1r,5s)-3-hydroxy-1-(1-hydroxy-2-methylpropyl)-4-methyl-6-oxa-2-azabicyclo[3.2.0]hept-2-en-7-one)

3D-SDF for NP0210687 ((1r,5s)-3-hydroxy-1-(1-hydroxy-2-methylpropyl)-4-methyl-6-oxa-2-azabicyclo[3.2.0]hept-2-en-7-one)

PDB for NP0210687 ((1r,5s)-3-hydroxy-1-(1-hydroxy-2-methylpropyl)-4-methyl-6-oxa-2-azabicyclo[3.2.0]hept-2-en-7-one)

3D PDB for NP0210687 ((1r,5s)-3-hydroxy-1-(1-hydroxy-2-methylpropyl)-4-methyl-6-oxa-2-azabicyclo[3.2.0]hept-2-en-7-one)

SMILES for NP0210687 ((1r,5s)-3-hydroxy-1-(1-hydroxy-2-methylpropyl)-4-methyl-6-oxa-2-azabicyclo[3.2.0]hept-2-en-7-one)

INCHI for NP0210687 ((1r,5s)-3-hydroxy-1-(1-hydroxy-2-methylpropyl)-4-methyl-6-oxa-2-azabicyclo[3.2.0]hept-2-en-7-one)

Structure for NP0210687 ((1r,5s)-3-hydroxy-1-(1-hydroxy-2-methylpropyl)-4-methyl-6-oxa-2-azabicyclo[3.2.0]hept-2-en-7-one)

3D Structure for NP0210687 ((1r,5s)-3-hydroxy-1-(1-hydroxy-2-methylpropyl)-4-methyl-6-oxa-2-azabicyclo[3.2.0]hept-2-en-7-one)