NP-MRD: Showing NP-Card for (2e,4e)-n-[(1s,2r)-2-hydroxy-1-{[(3z,5s,8s,10s)-2,7,10-trihydroxy-5-methyl-1,6-diazacyclododeca-1,3,6-trien-8-yl]-c-hydroxycarbonimidoyl}propyl]-9-methyldeca-2,4-dienimidic acid (NP0219243)

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Record Information

Version

2.0

Created at

2022-09-05 20:10:29 UTC

Updated at

2022-09-05 20:10:29 UTC

NP-MRD ID

NP0219243

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2e,4e)-n-[(1s,2r)-2-hydroxy-1-{[(3z,5s,8s,10s)-2,7,10-trihydroxy-5-methyl-1,6-diazacyclododeca-1,3,6-trien-8-yl]-c-hydroxycarbonimidoyl}propyl]-9-methyldeca-2,4-dienimidic acid

Description

Cepafungin III belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond. Based on a literature review very few articles have been published on Cepafungin III.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052222102D          

 36 36  0  0  1  0            999 V2000
   -5.0013   -8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.8579   -8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 34 36  1  6  0  0  0
M  END

     RDKit          3D

 78 78  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1652309052222102D          

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  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  4  0  0  0
 11 13  2  0  0  0  0
 14 13  1  1  0  0  0
 14 15  1  0  0  0  0
 15 16  1  4  0  0  0
 15 17  2  0  0  0  0
 18 17  1  1  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 24 23  1  4  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  1  0  0  0
 29 31  1  0  0  0  0
 31 32  2  0  0  0  0
 18 32  1  0  0  0  0
 32 33  1  4  0  0  0
 14 34  1  0  0  0  0
 34 35  1  0  0  0  0
 34 36  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0219243

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)CCC\C=C\C=C\C(O)=N[C@@H]([C@@H](C)O)C(O)=N[C@H]1C[C@@H](O)CCN=C(O)\C=C/[C@H](C)N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H42N4O6/c1-17(2)10-8-6-5-7-9-11-23(34)30-24(19(4)31)26(36)29-21-16-20(32)14-15-27-22(33)13-12-18(3)28-25(21)35/h5,7,9,11-13,17-21,24,31-32H,6,8,10,14-16H2,1-4H3,(H,27,33)(H,28,35)(H,29,36)(H,30,34)/b7-5+,11-9+,13-12-/t18-,19+,20-,21-,24-/m0/s1

> <INCHI_KEY>
ZQOSECHKDTUIEK-NUIZVSKESA-N

> <FORMULA>
C26H42N4O6

> <MOLECULAR_WEIGHT>
506.644

> <EXACT_MASS>
506.310435088

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
78

> <JCHEM_AVERAGE_POLARIZABILITY>
55.95260846091389

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2E,4E)-N-[(1S,2R)-2-hydroxy-1-{[(3Z,5S,8S,10S)-2,7,10-trihydroxy-5-methyl-1,6-diazacyclododeca-1,3,6-trien-8-yl]-C-hydroxycarbonimidoyl}propyl]-9-methyldeca-2,4-dienimidic acid

> <JCHEM_LOGP>
-1.927734184629117

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
-1.0542534210629109

> <JCHEM_PKA_STRONGEST_ACIDIC>
-7.074805754168868

> <JCHEM_PKA_STRONGEST_BASIC>
15.329504680294356

> <JCHEM_POLAR_SURFACE_AREA>
170.82

> <JCHEM_REFRACTIVITY>
142.19080000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2E,4E)-N-[(1S,2R)-2-hydroxy-1-{[(3Z,5S,8S,10S)-2,7,10-trihydroxy-5-methyl-1,6-diazacyclododeca-1,3,6-trien-8-yl]-C-hydroxycarbonimidoyl}propyl]-9-methyldeca-2,4-dienimidic acid

> <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      -9.336 -16.170   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -8.002 -15.400   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -8.002 -13.860   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -6.668 -16.170   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.335 -15.400   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.001 -16.170   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.667 -15.400   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.334 -16.170   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.000 -15.400   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334 -16.170   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667 -15.400   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.667 -13.860   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0       4.001 -16.170   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       5.335 -15.400   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.668 -16.170   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       6.668 -17.710   0.000  0.00  0.00           O+0
HETATM   17  N   UNK     0       8.002 -15.400   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0       9.336 -16.170   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      10.669 -15.400   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      10.669 -13.860   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       9.336 -13.090   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      12.003 -13.090   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      13.337 -13.860   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0      13.337 -15.400   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0      14.670 -16.170   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      16.004 -15.400   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      14.670 -17.710   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      13.337 -18.480   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      12.003 -17.710   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      12.003 -16.170   0.000  0.00  0.00           C+0
HETATM   31  N   UNK     0      10.669 -18.480   0.000  0.00  0.00           N+0
HETATM   32  C   UNK     0       9.336 -17.710   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       8.002 -18.480   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       5.335 -13.860   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       6.668 -13.090   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       4.001 -13.090   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   34                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19   32                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31   18   33                                                  
CONECT   33   32                                                            
CONECT   34   14   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₄₂N₄O₆

Average Mass

506.6440 Da

Monoisotopic Mass

506.31044 Da

IUPAC Name

(2E,4E)-N-[(1S,2R)-2-hydroxy-1-{[(3Z,5S,8S,10S)-2,7,10-trihydroxy-5-methyl-1,6-diazacyclododeca-1,3,6-trien-8-yl]-C-hydroxycarbonimidoyl}propyl]-9-methyldeca-2,4-dienimidic acid

Traditional Name

(2E,4E)-N-[(1S,2R)-2-hydroxy-1-{[(3Z,5S,8S,10S)-2,7,10-trihydroxy-5-methyl-1,6-diazacyclododeca-1,3,6-trien-8-yl]-C-hydroxycarbonimidoyl}propyl]-9-methyldeca-2,4-dienimidic acid

CAS Registry Number

Not Available

SMILES

CC(C)CCC\C=C\C=C\C(O)=N[C@@H]([C@@H](C)O)C(O)=N[C@H]1C[C@@H](O)CCN=C(O)\C=C/[C@H](C)N=C1O

InChI Identifier

InChI=1S/C26H42N4O6/c1-17(2)10-8-6-5-7-9-11-23(34)30-24(19(4)31)26(36)29-21-16-20(32)14-15-27-22(33)13-12-18(3)28-25(21)35/h5,7,9,11-13,17-21,24,31-32H,6,8,10,14-16H2,1-4H3,(H,27,33)(H,28,35)(H,29,36)(H,30,34)/b7-5+,11-9+,13-12-/t18-,19+,20-,21-,24-/m0/s1

InChI Key

ZQOSECHKDTUIEK-NUIZVSKESA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Dipeptides

Alternative Parents

Substituents

Alpha-dipeptide
Macrolactam
N-acyl-alpha amino acid or derivatives
Alpha-amino acid amide
N-substituted-alpha-amino acid
Alpha-amino acid or derivatives
Fatty amide
Fatty acyl
N-acyl-amine
Carboxamide group
Lactam
Secondary carboxylic acid amide
Secondary alcohol
Azacycle
Organoheterocyclic compound
Alcohol
Hydrocarbon derivative
Carbonyl group
Organic oxide
Organic oxygen compound
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
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
logP	-1.9	ChemAxon
pKa (Strongest Acidic)	-7.1	ChemAxon
pKa (Strongest Basic)	15.33	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	170.82 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	142.19 m³·mol⁻¹	ChemAxon
Polarizability	55.95 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	No	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

C00017600

Chemspider ID

4943722

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6439303

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2e,4e)-n-[(1s,2r)-2-hydroxy-1-{[(3z,5s,8s,10s)-2,7,10-trihydroxy-5-methyl-1,6-diazacyclododeca-1,3,6-trien-8-yl]-c-hydroxycarbonimidoyl}propyl]-9-methyldeca-2,4-dienimidic acid (NP0219243)

MOL for NP0219243 ((2e,4e)-n-[(1s,2r)-2-hydroxy-1-{[(3z,5s,8s,10s)-2,7,10-trihydroxy-5-methyl-1,6-diazacyclododeca-1,3,6-trien-8-yl]-c-hydroxycarbonimidoyl}propyl]-9-methyldeca-2,4-dienimidic acid)

3D MOL for NP0219243 ((2e,4e)-n-[(1s,2r)-2-hydroxy-1-{[(3z,5s,8s,10s)-2,7,10-trihydroxy-5-methyl-1,6-diazacyclododeca-1,3,6-trien-8-yl]-c-hydroxycarbonimidoyl}propyl]-9-methyldeca-2,4-dienimidic acid)

3D SDF for NP0219243 ((2e,4e)-n-[(1s,2r)-2-hydroxy-1-{[(3z,5s,8s,10s)-2,7,10-trihydroxy-5-methyl-1,6-diazacyclododeca-1,3,6-trien-8-yl]-c-hydroxycarbonimidoyl}propyl]-9-methyldeca-2,4-dienimidic acid)

3D-SDF for NP0219243 ((2e,4e)-n-[(1s,2r)-2-hydroxy-1-{[(3z,5s,8s,10s)-2,7,10-trihydroxy-5-methyl-1,6-diazacyclododeca-1,3,6-trien-8-yl]-c-hydroxycarbonimidoyl}propyl]-9-methyldeca-2,4-dienimidic acid)

PDB for NP0219243 ((2e,4e)-n-[(1s,2r)-2-hydroxy-1-{[(3z,5s,8s,10s)-2,7,10-trihydroxy-5-methyl-1,6-diazacyclododeca-1,3,6-trien-8-yl]-c-hydroxycarbonimidoyl}propyl]-9-methyldeca-2,4-dienimidic acid)

3D PDB for NP0219243 ((2e,4e)-n-[(1s,2r)-2-hydroxy-1-{[(3z,5s,8s,10s)-2,7,10-trihydroxy-5-methyl-1,6-diazacyclododeca-1,3,6-trien-8-yl]-c-hydroxycarbonimidoyl}propyl]-9-methyldeca-2,4-dienimidic acid)

SMILES for NP0219243 ((2e,4e)-n-[(1s,2r)-2-hydroxy-1-{[(3z,5s,8s,10s)-2,7,10-trihydroxy-5-methyl-1,6-diazacyclododeca-1,3,6-trien-8-yl]-c-hydroxycarbonimidoyl}propyl]-9-methyldeca-2,4-dienimidic acid)

INCHI for NP0219243 ((2e,4e)-n-[(1s,2r)-2-hydroxy-1-{[(3z,5s,8s,10s)-2,7,10-trihydroxy-5-methyl-1,6-diazacyclododeca-1,3,6-trien-8-yl]-c-hydroxycarbonimidoyl}propyl]-9-methyldeca-2,4-dienimidic acid)

Structure for NP0219243 ((2e,4e)-n-[(1s,2r)-2-hydroxy-1-{[(3z,5s,8s,10s)-2,7,10-trihydroxy-5-methyl-1,6-diazacyclododeca-1,3,6-trien-8-yl]-c-hydroxycarbonimidoyl}propyl]-9-methyldeca-2,4-dienimidic acid)

3D Structure for NP0219243 ((2e,4e)-n-[(1s,2r)-2-hydroxy-1-{[(3z,5s,8s,10s)-2,7,10-trihydroxy-5-methyl-1,6-diazacyclododeca-1,3,6-trien-8-yl]-c-hydroxycarbonimidoyl}propyl]-9-methyldeca-2,4-dienimidic acid)