NP-MRD: Showing NP-Card for (4r,7r,8r,9e,14z,16e,18s,20s)-2,11,18,20-tetrahydroxy-7-isopropyl-4,8,16-trimethyl-6,23-dioxa-3,12,25-triazabicyclo[20.2.1]pentacosa-1(24),2,9,11,14,16,22(25)-heptaen-5-one (NP0234357)

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Record Information

Version

2.0

Created at

2022-09-06 16:20:46 UTC

Updated at

2022-09-06 16:20:46 UTC

NP-MRD ID

NP0234357

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(4r,7r,8r,9e,14z,16e,18s,20s)-2,11,18,20-tetrahydroxy-7-isopropyl-4,8,16-trimethyl-6,23-dioxa-3,12,25-triazabicyclo[20.2.1]pentacosa-1(24),2,9,11,14,16,22(25)-heptaen-5-one

Description

Madumycin II 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. (4r,7r,8r,9e,14z,16e,18s,20s)-2,11,18,20-tetrahydroxy-7-isopropyl-4,8,16-trimethyl-6,23-dioxa-3,12,25-triazabicyclo[20.2.1]pentacosa-1(24),2,9,11,14,16,22(25)-heptaen-5-one is found in Actinoplanes philippinensis. (4r,7r,8r,9e,14z,16e,18s,20s)-2,11,18,20-tetrahydroxy-7-isopropyl-4,8,16-trimethyl-6,23-dioxa-3,12,25-triazabicyclo[20.2.1]pentacosa-1(24),2,9,11,14,16,22(25)-heptaen-5-one was first documented in 2017 (PMID: 28505372). Based on a literature review very few articles have been published on Madumycin II.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062218202D          

 36 37  0  0  1  0            999 V2000
    6.5933   -0.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309062218202D          

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  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 10 14  1  0  0  0  0
 12 15  1  0  0  0  0
 15 16  1  4  0  0  0
 15 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  6  0  0  0
 18 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  6  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 23 27  1  0  0  0  0
 27 28  1  6  0  0  0
 27 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 31 33  2  0  0  0  0
 33 34  1  4  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
  2 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0234357

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)[C@H]1OC(=O)[C@@H](C)N=C(O)C2=COC(C[C@@H](O)C[C@H](O)\C=C(/C)\C=C/CN=C(O)\C=C\[C@H]1C)=N2

> <INCHI_IDENTIFIER>
InChI=1S/C26H37N3O7/c1-15(2)24-17(4)8-9-22(32)27-10-6-7-16(3)11-19(30)12-20(31)13-23-29-21(14-35-23)25(33)28-18(5)26(34)36-24/h6-9,11,14-15,17-20,24,30-31H,10,12-13H2,1-5H3,(H,27,32)(H,28,33)/b7-6-,9-8+,16-11+/t17-,18-,19-,20+,24-/m1/s1

> <INCHI_KEY>
SAQNYTQFLPVTNJ-YHZICBGDSA-N

> <FORMULA>
C26H37N3O7

> <MOLECULAR_WEIGHT>
503.596

> <EXACT_MASS>
503.263150543

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
53.184808703069635

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R,7R,8R,9E,14Z,16E,18S,20S)-2,11,18,20-tetrahydroxy-4,8,16-trimethyl-7-(propan-2-yl)-6,23-dioxa-3,12,25-triazabicyclo[20.2.1]pentacosa-1(24),2,9,11,14,16,22(25)-heptaen-5-one

> <JCHEM_LOGP>
2.897468638666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
7.76392814020501

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.632547279559789

> <JCHEM_PKA_STRONGEST_BASIC>
4.630978736227308

> <JCHEM_POLAR_SURFACE_AREA>
157.97000000000003

> <JCHEM_REFRACTIVITY>
136.89029999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(4R,7R,8R,9E,14Z,16E,18S,20S)-2,11,18,20-tetrahydroxy-7-isopropyl-4,8,16-trimethyl-6,23-dioxa-3,12,25-triazabicyclo[20.2.1]pentacosa-1(24),2,9,11,14,16,22(25)-heptaen-5-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0      12.307  -1.358   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.319  -2.519   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      12.569  -3.863   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      11.058  -3.565   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       9.928  -4.612   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      10.875  -2.036   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.656  -0.872   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       8.188  -1.338   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       9.954   0.638   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.795   1.652   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       9.093   3.163   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       7.934   4.177   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.758   3.087   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       7.255   1.630   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       8.232   5.688   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       9.690   6.185   0.000  0.00  0.00           O+0
HETATM   17  N   UNK     0       7.073   6.701   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0       7.372   8.212   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.212   9.226   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.829   8.709   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       9.128  10.220   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       9.988   7.695   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      11.446   8.192   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      11.744   9.703   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.585  10.717   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      13.202  10.200   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      12.605   7.179   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      14.063   7.676   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      12.307   5.668   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      13.466   4.654   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      13.168   3.143   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      11.710   2.646   0.000  0.00  0.00           O+0
HETATM   33  N   UNK     0      14.327   2.129   0.000  0.00  0.00           N+0
HETATM   34  C   UNK     0      14.028   0.618   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      15.188  -0.395   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      14.889  -1.906   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   36                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   14                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13   10                                                       
CONECT   15   12   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24   27                                                  
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24                                                            
CONECT   27   23   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35    2                                                       
MASTER        0    0    0    0    0    0    0    0   36    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₃₇N₃O₇

Average Mass

503.5960 Da

Monoisotopic Mass

503.26315 Da

IUPAC Name

(4R,7R,8R,9E,14Z,16E,18S,20S)-2,11,18,20-tetrahydroxy-4,8,16-trimethyl-7-(propan-2-yl)-6,23-dioxa-3,12,25-triazabicyclo[20.2.1]pentacosa-1(24),2,9,11,14,16,22(25)-heptaen-5-one

Traditional Name

(4R,7R,8R,9E,14Z,16E,18S,20S)-2,11,18,20-tetrahydroxy-7-isopropyl-4,8,16-trimethyl-6,23-dioxa-3,12,25-triazabicyclo[20.2.1]pentacosa-1(24),2,9,11,14,16,22(25)-heptaen-5-one

CAS Registry Number

Not Available

SMILES

CC(C)[C@H]1OC(=O)[C@@H](C)N=C(O)C2=COC(C[C@@H](O)C[C@H](O)\C=C(/C)\C=C/CN=C(O)\C=C\[C@H]1C)=N2

InChI Identifier

InChI=1S/C26H37N3O7/c1-15(2)24-17(4)8-9-22(32)27-10-6-7-16(3)11-19(30)12-20(31)13-23-29-21(14-35-23)25(33)28-18(5)26(34)36-24/h6-9,11,14-15,17-20,24,30-31H,10,12-13H2,1-5H3,(H,27,32)(H,28,33)/b7-6-,9-8+,16-11+/t17-,18-,19-,20+,24-/m1/s1

InChI Key

SAQNYTQFLPVTNJ-YHZICBGDSA-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
Actinoplanes philippinensis	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
Alpha-amino acid ester
Alpha-amino acid or derivatives
Heteroaromatic compound
Cyclic carboximidic acid
Oxazole
Azole
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	2.9	ChemAxon
pKa (Strongest Acidic)	6.63	ChemAxon
pKa (Strongest Basic)	4.63	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	157.97 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	136.89 m³·mol⁻¹	ChemAxon
Polarizability	53.18 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

137349724

PDB ID

M2D

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Osterman IA, Khabibullina NF, Komarova ES, Kasatsky P, Kartsev VG, Bogdanov AA, Dontsova OA, Konevega AL, Sergiev PV, Polikanov YS: Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state. Nucleic Acids Res. 2017 Jul 7;45(12):7507-7514. doi: 10.1093/nar/gkx413. [PubMed:28505372 ]
LOTUS database [Link]

Showing NP-Card for (4r,7r,8r,9e,14z,16e,18s,20s)-2,11,18,20-tetrahydroxy-7-isopropyl-4,8,16-trimethyl-6,23-dioxa-3,12,25-triazabicyclo[20.2.1]pentacosa-1(24),2,9,11,14,16,22(25)-heptaen-5-one (NP0234357)

MOL for NP0234357 ((4r,7r,8r,9e,14z,16e,18s,20s)-2,11,18,20-tetrahydroxy-7-isopropyl-4,8,16-trimethyl-6,23-dioxa-3,12,25-triazabicyclo[20.2.1]pentacosa-1(24),2,9,11,14,16,22(25)-heptaen-5-one)

3D MOL for NP0234357 ((4r,7r,8r,9e,14z,16e,18s,20s)-2,11,18,20-tetrahydroxy-7-isopropyl-4,8,16-trimethyl-6,23-dioxa-3,12,25-triazabicyclo[20.2.1]pentacosa-1(24),2,9,11,14,16,22(25)-heptaen-5-one)

3D SDF for NP0234357 ((4r,7r,8r,9e,14z,16e,18s,20s)-2,11,18,20-tetrahydroxy-7-isopropyl-4,8,16-trimethyl-6,23-dioxa-3,12,25-triazabicyclo[20.2.1]pentacosa-1(24),2,9,11,14,16,22(25)-heptaen-5-one)

3D-SDF for NP0234357 ((4r,7r,8r,9e,14z,16e,18s,20s)-2,11,18,20-tetrahydroxy-7-isopropyl-4,8,16-trimethyl-6,23-dioxa-3,12,25-triazabicyclo[20.2.1]pentacosa-1(24),2,9,11,14,16,22(25)-heptaen-5-one)

PDB for NP0234357 ((4r,7r,8r,9e,14z,16e,18s,20s)-2,11,18,20-tetrahydroxy-7-isopropyl-4,8,16-trimethyl-6,23-dioxa-3,12,25-triazabicyclo[20.2.1]pentacosa-1(24),2,9,11,14,16,22(25)-heptaen-5-one)

3D PDB for NP0234357 ((4r,7r,8r,9e,14z,16e,18s,20s)-2,11,18,20-tetrahydroxy-7-isopropyl-4,8,16-trimethyl-6,23-dioxa-3,12,25-triazabicyclo[20.2.1]pentacosa-1(24),2,9,11,14,16,22(25)-heptaen-5-one)

SMILES for NP0234357 ((4r,7r,8r,9e,14z,16e,18s,20s)-2,11,18,20-tetrahydroxy-7-isopropyl-4,8,16-trimethyl-6,23-dioxa-3,12,25-triazabicyclo[20.2.1]pentacosa-1(24),2,9,11,14,16,22(25)-heptaen-5-one)

INCHI for NP0234357 ((4r,7r,8r,9e,14z,16e,18s,20s)-2,11,18,20-tetrahydroxy-7-isopropyl-4,8,16-trimethyl-6,23-dioxa-3,12,25-triazabicyclo[20.2.1]pentacosa-1(24),2,9,11,14,16,22(25)-heptaen-5-one)

Structure for NP0234357 ((4r,7r,8r,9e,14z,16e,18s,20s)-2,11,18,20-tetrahydroxy-7-isopropyl-4,8,16-trimethyl-6,23-dioxa-3,12,25-triazabicyclo[20.2.1]pentacosa-1(24),2,9,11,14,16,22(25)-heptaen-5-one)

3D Structure for NP0234357 ((4r,7r,8r,9e,14z,16e,18s,20s)-2,11,18,20-tetrahydroxy-7-isopropyl-4,8,16-trimethyl-6,23-dioxa-3,12,25-triazabicyclo[20.2.1]pentacosa-1(24),2,9,11,14,16,22(25)-heptaen-5-one)