NP-MRD: Showing NP-Card for neomethymycin (NP0202535)

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Record Information

Version

2.0

Created at

2022-09-04 21:46:01 UTC

Updated at

2022-09-04 21:46:02 UTC

NP-MRD ID

NP0202535

Secondary Accession Numbers

None

Natural Product Identification

Common Name

neomethymycin

Description

Neomethymycin belongs to the class of organic compounds known as aminoglycosides. These are molecules or a portion of a molecule composed of amino-modified sugars. Thus, neomethymycin is considered to be a macrolide. Neomethymycin is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. neomethymycin is found in Streptomyces venezuelae. neomethymycin was first documented in 2007 (PMID: 17049185). Based on a literature review a small amount of articles have been published on neomethymycin (PMID: 23866020) (PMID: 22737401) (PMID: 20695498) (PMID: 19746907).

Structure

MOL 3D MOL SDF PDB SMILES InChI

  Mrv1652309042223462D          

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M  END

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M  END
> <DATABASE_ID>
NP0202535

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C25H43NO7/c1-13-9-10-20(28)14(2)11-15(3)22(17(5)24(30)32-23(13)18(6)27)33-25-21(29)19(26(7)8)12-16(4)31-25/h9-10,13-19,21-23,25,27,29H,11-12H2,1-8H3/b10-9+/t13-,14-,15+,16-,17-,18-,19+,21-,22+,23+,25+/m1/s1

> <INCHI_KEY>
UEIVQYHYALXCBD-OTUJEKPESA-N

> <FORMULA>
C25H43NO7

> <MOLECULAR_WEIGHT>
469.619

> <EXACT_MASS>
469.303952729

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
51.64275281525286

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4S,5S,7R,9E,11R,12S)-4-{[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy}-12-[(1R)-1-hydroxyethyl]-3,5,7,11-tetramethyl-1-oxacyclododec-9-ene-2,8-dione

> <JCHEM_LOGP>
3.1266004863333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.468395939668788

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.821923457560867

> <JCHEM_PKA_STRONGEST_BASIC>
8.380997890363863

> <JCHEM_POLAR_SURFACE_AREA>
105.53000000000002

> <JCHEM_REFRACTIVITY>
125.73809999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
neomethymycin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.000   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334   2.310   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       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.668  -0.770   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   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0      -2.667  -7.700   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0      -2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -2.667  -4.620   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   21                                                  
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                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   16                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   12   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19    2   22                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   32                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   29   32                                                  
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29                                                            
CONECT   32   28   23   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

C₂₅H₄₃NO₇

Average Mass

469.6190 Da

Monoisotopic Mass

469.30395 Da

IUPAC Name

(3R,4S,5S,7R,9E,11R,12S)-4-{[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy}-12-[(1R)-1-hydroxyethyl]-3,5,7,11-tetramethyl-1-oxacyclododec-9-ene-2,8-dione

Traditional Name

neomethymycin

CAS Registry Number

Not Available

SMILES

C[C@@H](O)[C@H]1OC(=O)[C@H](C)[C@@H](O[C@@H]2O[C@H](C)C[C@@H]([C@H]2O)N(C)C)[C@@H](C)C[C@@H](C)C(=O)\C=C\[C@H]1C

InChI Identifier

InChI=1S/C25H43NO7/c1-13-9-10-20(28)14(2)11-15(3)22(17(5)24(30)32-23(13)18(6)27)33-25-21(29)19(26(7)8)12-16(4)31-25/h9-10,13-19,21-23,25,27,29H,11-12H2,1-8H3/b10-9+/t13-,14-,15+,16-,17-,18-,19+,21-,22+,23+,25+/m1/s1

InChI Key

UEIVQYHYALXCBD-OTUJEKPESA-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 venezuelae	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aminoglycosides. These are molecules or a portion of a molecule composed of amino-modified sugars.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Aminoglycosides

Alternative Parents

Substituents

Aminoglycoside core
Macrolide
Oxane
1,2-aminoalcohol
Amino acid or derivatives
Carboxylic acid ester
Ketone
Lactone
Secondary alcohol
Tertiary amine
Tertiary aliphatic amine
Cyclic ketone
Monocarboxylic acid or derivatives
Acetal
Carboxylic acid derivative
Organoheterocyclic compound
Oxacycle
Organopnictogen compound
Amine
Alcohol
Organonitrogen compound
Organic oxide
Organic nitrogen compound
Carbonyl group
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

macrolide antibiotic (CHEBI:29656 )
monosaccharide derivative (CHEBI:29656 )
enone (CHEBI:29656 )
Macrolides and lactone polyketides (C11995 )
Macrolides and lactone polyketides (LMPK04000036 )

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	3.13	ChemAxon
pKa (Strongest Acidic)	12.82	ChemAxon
pKa (Strongest Basic)	8.38	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	105.53 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	125.74 m³·mol⁻¹	ChemAxon
Polarizability	51.64 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

4445263

KEGG Compound ID

C11995

BioCyc ID

CPD-13833

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5282033

PDB ID

Not Available

ChEBI ID

29656

Good Scents ID

Not Available

References

General References

Hansen DA, Rath CM, Eisman EB, Narayan AR, Kittendorf JD, Mortison JD, Yoon YJ, Sherman DH: Biocatalytic synthesis of pikromycin, methymycin, neomethymycin, novamethymycin, and ketomethymycin. J Am Chem Soc. 2013 Jul 31;135(30):11232-8. doi: 10.1021/ja404134f. Epub 2013 Jul 18. [PubMed:23866020 ]
Shareef AR, Sherman DH, Montgomery J: Nickel-Catalyzed Regiodivergent Approach to Macrolide Motifs. Chem Sci. 2012 Jan 1;3(3):892-895. doi: 10.1039/C2SC00866A. Epub 2011 Dec 6. [PubMed:22737401 ]
Borisova SA, Liu HW: Characterization of glycosyltransferase DesVII and its auxiliary partner protein DesVIII in the methymycin/picromycin biosynthetic pathway. Biochemistry. 2010 Sep 21;49(37):8071-84. doi: 10.1021/bi1007657. [PubMed:20695498 ]
Szu PH, Ruszczycky MW, Choi SH, Yan F, Liu HW: Characterization and mechanistic studies of DesII: a radical S-adenosyl-L-methionine enzyme involved in the biosynthesis of TDP-D-desosamine. J Am Chem Soc. 2009 Oct 7;131(39):14030-42. doi: 10.1021/ja903354k. [PubMed:19746907 ]
Hong JS, Park SJ, Parajuli N, Park SR, Koh HS, Jung WS, Choi CY, Yoon YJ: Functional analysis of desVIII homologues involved in glycosylation of macrolide antibiotics by interspecies complementation. Gene. 2007 Jan 15;386(1-2):123-30. doi: 10.1016/j.gene.2006.08.021. Epub 2006 Sep 12. [PubMed:17049185 ]
LOTUS database [Link]

Showing NP-Card for neomethymycin (NP0202535)

MOL for NP0202535 (neomethymycin)

3D MOL for NP0202535 (neomethymycin)

3D SDF for NP0202535 (neomethymycin)

3D-SDF for NP0202535 (neomethymycin)

PDB for NP0202535 (neomethymycin)

3D PDB for NP0202535 (neomethymycin)

SMILES for NP0202535 (neomethymycin)

INCHI for NP0202535 (neomethymycin)

Structure for NP0202535 (neomethymycin)

3D Structure for NP0202535 (neomethymycin)