NP-MRD: Showing NP-Card for Methylenomycin A (NP0021492)

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Record Information

Version

1.0

Created at

2021-01-06 06:46:26 UTC

Updated at

2021-07-15 17:36:30 UTC

NP-MRD ID

NP0021492

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Methylenomycin A

Provided By

NPAtlas

Description

Methylenomycin A is found in Streptomyces albidoflavus, Streptomyces coelicolor, Streptomyces parvulus, Streptomyces sp., Streptomyces violaceoruber, Streptomyces violaceusniger No.2416 and Streptomyces virginiae. It was first documented in 1974 (PMID: 4853334). Based on a literature review very few articles have been published on (1R,2S,5R)-1,5-dimethyl-3-methylidene-4-oxo-6-oxabicyclo[3.1.0]Hexane-2-carboxylic acid.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242105163D          

 23 24  0  0  0  0            999 V2000
   -1.7464    1.9608    0.2582 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9214    0.9436    0.5574 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3067    1.0043    1.3414 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5696    1.8677    2.2226 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2140   -0.0832    0.9702 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6525    0.2311    0.6539 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9409   -1.4000    1.2062 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3873   -0.8990    0.0367 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9914   -1.2002   -1.2903 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0470   -0.4853    0.1716 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8510   -0.7226   -1.0281 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4193   -1.2662   -2.0832 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1841   -0.3349   -1.0395 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5090    2.9304    0.6156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6259    1.8119   -0.3260 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3410   -0.5990    0.9189 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8064    0.5776   -0.3791 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9345    1.0968    1.3177 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1050   -1.1775   -1.1745 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7508   -0.3993   -2.0295 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6800   -2.1960   -1.6451 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5295   -0.9894    1.0497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8465   -0.6715   -0.3250 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  6  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 10  2  1  0  0  0  0
  8  5  1  0  0  0  0
  1 14  1  0  0  0  0
  1 15  1  0  0  0  0
  6 16  1  0  0  0  0
  6 17  1  0  0  0  0
  6 18  1  0  0  0  0
  9 19  1  0  0  0  0
  9 20  1  0  0  0  0
  9 21  1  0  0  0  0
 10 22  1  1  0  0  0
 13 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0021492

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)[C@]1([H])C(=C([H])[H])C(=O)[C@]2(O[C@@]12C([H])([H])[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C9H10O4/c1-4-5(7(11)12)8(2)9(3,13-8)6(4)10/h5H,1H2,2-3H3,(H,11,12)/t5-,8-,9+/m0/s1

> <INCHI_KEY>
HBECYYFDLZZMPL-CGMLFGJQSA-N

> <FORMULA>
C9H10O4

> <MOLECULAR_WEIGHT>
182.175

> <EXACT_MASS>
182.057908802

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
17.176025598422164

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2R,5S)-1,5-dimethyl-3-methylidene-4-oxo-6-oxabicyclo[3.1.0]hexane-2-carboxylic acid

> <ALOGPS_LOGP>
0.86

> <JCHEM_LOGP>
0.8026618213333336

> <ALOGPS_LOGS>
-0.83

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
18.406689963621798

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.952988687547176

> <JCHEM_PKA_STRONGEST_BASIC>
-4.3119591245834945

> <JCHEM_POLAR_SURFACE_AREA>
66.9

> <JCHEM_REFRACTIVITY>
42.8053

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.69e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methylenomycin A

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0      -1.746   1.961   0.258  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.921   0.944   0.557  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.307   1.004   1.341  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.570   1.868   2.223  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.214  -0.083   0.970  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.652   0.231   0.654  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.941  -1.400   1.206  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.387  -0.899   0.037  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.991  -1.200  -1.290  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.047  -0.485   0.172  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.851  -0.723  -1.028  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.419  -1.266  -2.083  0.00  0.00           O+0
HETATM   13  O   UNK     0      -3.184  -0.335  -1.040  0.00  0.00           O+0
HETATM   14  H   UNK     0      -1.509   2.930   0.616  0.00  0.00           H+0
HETATM   15  H   UNK     0      -2.626   1.812  -0.326  0.00  0.00           H+0
HETATM   16  H   UNK     0       3.341  -0.599   0.919  0.00  0.00           H+0
HETATM   17  H   UNK     0       2.806   0.578  -0.379  0.00  0.00           H+0
HETATM   18  H   UNK     0       2.934   1.097   1.318  0.00  0.00           H+0
HETATM   19  H   UNK     0       2.105  -1.178  -1.175  0.00  0.00           H+0
HETATM   20  H   UNK     0       0.751  -0.399  -2.030  0.00  0.00           H+0
HETATM   21  H   UNK     0       0.680  -2.196  -1.645  0.00  0.00           H+0
HETATM   22  H   UNK     0      -1.530  -0.989   1.050  0.00  0.00           H+0
HETATM   23  H   UNK     0      -3.846  -0.672  -0.325  0.00  0.00           H+0
CONECT    1    2   14   15                                                  
CONECT    2    1    3   10                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7    8                                             
CONECT    6    5   16   17   18                                             
CONECT    7    5    8                                                       
CONECT    8    7    9   10    5                                             
CONECT    9    8   19   20   21                                             
CONECT   10    8   11    2   22                                             
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   23                                                       
CONECT   14    1                                                            
CONECT   15    1                                                            
CONECT   16    6                                                            
CONECT   17    6                                                            
CONECT   18    6                                                            
CONECT   19    9                                                            
CONECT   20    9                                                            
CONECT   21    9                                                            
CONECT   22   10                                                            
CONECT   23   13                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
(1R,2S,5R)-1,5-Dimethyl-3-methylidene-4-oxo-6-oxabicyclo[3.1.0]hexane-2-carboxylate	Generator

Chemical Formula

C₉H₁₀O₄

Average Mass

182.1750 Da

Monoisotopic Mass

182.05791 Da

IUPAC Name

(1S,2R,5S)-1,5-dimethyl-3-methylidene-4-oxo-6-oxabicyclo[3.1.0]hexane-2-carboxylic acid

Traditional Name

methylenomycin A

CAS Registry Number

Not Available

SMILES

C[C@]12O[C@@]1(C)C(=O)C(=C)[C@@H]2C(O)=O

InChI Identifier

InChI=1S/C9H10O4/c1-4-5(7(11)12)8(2)9(3,13-8)6(4)10/h5H,1H2,2-3H3,(H,11,12)/t5-,8-,9+/m1/s1

InChI Key

HBECYYFDLZZMPL-CGMLFGJQSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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 albidoflavus	LOTUS Database	35616633
Streptomyces coelicolor	LOTUS Database	35616633
Streptomyces parvulus	LOTUS Database	35616633
Streptomyces sp.	NPAtlas	4853334
Streptomyces violaceoruber	LOTUS Database	35616633
Streptomyces violaceusniger No.2416	Bacteria	KNApSAcK
Streptomyces virginiae	LOTUS Database	35616633

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	0.86	ALOGPS
logP	0.8	ChemAxon
logS	-0.83	ALOGPS
pKa (Strongest Acidic)	3.95	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	66.9 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	42.81 m³·mol⁻¹	ChemAxon
Polarizability	17.18 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

NPAtlas ID

NPA009598

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

61679571

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14240209

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Haneishi T, Terahara A, Arai M, Hata T, Tamura C: New antibiotics, methylenomycins A and B. II. Structures of methylenomycins A and B. J Antibiot (Tokyo). 1974 Jun;27(6):393-9. doi: 10.7164/antibiotics.27.393. [PubMed:4853334 ]

Showing NP-Card for Methylenomycin A (NP0021492)

MOL for NP0021492 (Methylenomycin A)

3D MOL for NP0021492 (Methylenomycin A)

3D SDF for NP0021492 (Methylenomycin A)

3D-SDF for NP0021492 (Methylenomycin A)

PDB for NP0021492 (Methylenomycin A)

3D PDB for NP0021492 (Methylenomycin A)

SMILES for NP0021492 (Methylenomycin A)

INCHI for NP0021492 (Methylenomycin A)

Structure for NP0021492 (Methylenomycin A)

3D Structure for NP0021492 (Methylenomycin A)