NP-MRD: Showing NP-Card for Detoxin D4 (NP0062013)

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Record Information

Version

2.0

Created at

2022-04-28 06:41:57 UTC

Updated at

2022-04-28 06:41:57 UTC

NP-MRD ID

NP0062013

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Detoxin D4

Description

(3R)-3-[(2R,3S)-1-[(2R)-2-amino-3-methylbutanoyl]-3-(butanoyloxy)pyrrolidin-2-yl]-3-{[(2S)-2-{[(2R)-1-hydroxy-2-methylbutylidene]amino}-3-phenylpropanoyl]oxy}propanoic acid belongs to the class of organic compounds known as depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids), commonly but not necessarily regularly alternating. Detoxin D4 is found in Streptomyces caespitosus. Based on a literature review very few articles have been published on (3R)-3-[(2R,3S)-1-[(2R)-2-amino-3-methylbutanoyl]-3-(butanoyloxy)pyrrolidin-2-yl]-3-{[(2S)-2-{[(2R)-1-hydroxy-2-methylbutylidene]amino}-3-phenylpropanoyl]oxy}propanoic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282208412D          

 41 42  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652304282208412D          

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    6.4492    4.5030    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5724   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4723   -1.7895    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  3  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  1  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
  4 15  1  1  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
  2 21  1  1  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
 24 25  1  6  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
 28 29  1  6  0  0  0
 28 30  1  0  0  0  0
 30 31  1  0  0  0  0
 24 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
 33 38  1  0  0  0  0
  1 39  1  0  0  0  0
 39 40  2  0  0  0  0
 39 41  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0062013

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCC(=O)O[C@H]1CCN([C@H]1[C@@H](CC(O)=O)OC(=O)[C@H](CC1=CC=CC=C1)NC(=O)[C@H](C)CC)C(=O)[C@H](N)C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C30H45N3O8/c1-6-11-25(36)40-22-14-15-33(29(38)26(31)18(3)4)27(22)23(17-24(34)35)41-30(39)21(32-28(37)19(5)7-2)16-20-12-9-8-10-13-20/h8-10,12-13,18-19,21-23,26-27H,6-7,11,14-17,31H2,1-5H3,(H,32,37)(H,34,35)/t19-,21+,22+,23-,26-,27-/m1/s1

> <INCHI_KEY>
MVVOKRBJEDFUGJ-YOTWSEIZSA-N

> <FORMULA>
C30H45N3O8

> <MOLECULAR_WEIGHT>
575.703

> <EXACT_MASS>
575.320665421

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
86

> <JCHEM_AVERAGE_POLARIZABILITY>
61.118572513336645

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R)-3-[(2R,3S)-1-[(2R)-2-amino-3-methylbutanoyl]-3-(butanoyloxy)pyrrolidin-2-yl]-3-{[(2S)-2-[(2R)-2-methylbutanamido]-3-phenylpropanoyl]oxy}propanoic acid

> <ALOGPS_LOGP>
0.33

> <JCHEM_LOGP>
0.9224074595876957

> <ALOGPS_LOGS>
-4.31

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.202666287002643

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.797159319847239

> <JCHEM_PKA_STRONGEST_BASIC>
8.506587826884541

> <JCHEM_POLAR_SURFACE_AREA>
165.32999999999998

> <JCHEM_REFRACTIVITY>
149.63379999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
17

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.82e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R)-3-[(2R,3S)-1-[(2R)-2-amino-3-methylbutanoyl]-3-(butanoyloxy)pyrrolidin-2-yl]-3-{[(2S)-2-[(2R)-2-methylbutanamido]-3-phenylpropanoyl]oxy}propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      13.337  -1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.337  -0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      14.670   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      14.831   2.302   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      16.338   2.622   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      17.108   1.288   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      16.077   0.144   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      16.398  -1.363   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      15.253  -2.393   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      17.862  -1.839   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      18.182  -3.345   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      19.007  -0.808   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      18.686   0.698   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      20.471  -1.284   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      13.687   3.332   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      14.007   4.838   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      15.472   5.314   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      12.863   5.869   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      13.183   7.375   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      12.038   8.406   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      12.003   0.770   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      10.669   0.000   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       9.336   0.770   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      10.669  -1.540   0.000  0.00  0.00           C+0
HETATM   25  N   UNK     0       9.336  -2.310   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0       8.002  -1.540   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       8.002   0.000   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.668  -3.850   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.335  -1.540   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      12.003  -2.310   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      12.003  -3.850   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      13.337  -4.620   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      13.337  -6.160   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      12.003  -6.930   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      10.669  -6.160   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      14.670  -2.310   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0      15.815  -3.340   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0      14.670  -3.850   0.000  0.00  0.00           O+0
CONECT    1    2   39                                                       
CONECT    2    1    3   21                                                  
CONECT    3    2    4    7                                                  
CONECT    4    3    5   15                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    3    8                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15    4   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19                                                            
CONECT   21    2   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25   32                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30                                                            
CONECT   32   24   33                                                       
CONECT   33   32   34   38                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   33                                                       
CONECT   39    1   40   41                                                  
CONECT   40   39                                                            
CONECT   41   39                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   84    0
END

View in JSmol

Synonyms

Value	Source
(3R)-3-[(2R,3S)-1-[(2R)-2-Amino-3-methylbutanoyl]-3-(butanoyloxy)pyrrolidin-2-yl]-3-{[(2S)-2-{[(2R)-1-hydroxy-2-methylbutylidene]amino}-3-phenylpropanoyl]oxy}propanoate	Generator

Chemical Formula

C₃₀H₄₅N₃O₈

Average Mass

575.7030 Da

Monoisotopic Mass

575.32067 Da

IUPAC Name

(3R)-3-[(2R,3S)-1-[(2R)-2-amino-3-methylbutanoyl]-3-(butanoyloxy)pyrrolidin-2-yl]-3-{[(2S)-2-[(2R)-2-methylbutanamido]-3-phenylpropanoyl]oxy}propanoic acid

Traditional Name

(3R)-3-[(2R,3S)-1-[(2R)-2-amino-3-methylbutanoyl]-3-(butanoyloxy)pyrrolidin-2-yl]-3-{[(2S)-2-[(2R)-2-methylbutanamido]-3-phenylpropanoyl]oxy}propanoic acid

CAS Registry Number

Not Available

SMILES

CCCC(=O)O[C@H]1CCN([C@H]1[C@@H](CC(O)=O)OC(=O)[C@H](CC1=CC=CC=C1)NC(=O)[C@H](C)CC)C(=O)[C@H](N)C(C)C

InChI Identifier

InChI=1S/C30H45N3O8/c1-6-11-25(36)40-22-14-15-33(29(38)26(31)18(3)4)27(22)23(17-24(34)35)41-30(39)21(32-28(37)19(5)7-2)16-20-12-9-8-10-13-20/h8-10,12-13,18-19,21-23,26-27H,6-7,11,14-17,31H2,1-5H3,(H,32,37)(H,34,35)/t19-,21+,22+,23-,26-,27-/m1/s1

InChI Key

MVVOKRBJEDFUGJ-YOTWSEIZSA-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 caespitosus	Bacteria	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids), commonly but not necessarily regularly alternating.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Peptidomimetics

Sub Class

Depsipeptides

Direct Parent

Depsipeptides

Alternative Parents

Substituents

Depsipeptide
Phenylalanine or derivatives
Valine or derivatives
N-acyl-alpha amino acid or derivatives
Alpha-amino acid ester
Alpha-amino acid amide
Amphetamine or derivatives
Alpha-amino acid or derivatives
Tricarboxylic acid or derivatives
N-acylpyrrolidine
Fatty acid ester
Fatty acyl
Benzenoid
Monocyclic benzene moiety
Tertiary carboxylic acid amide
Pyrrolidine
Amino acid
Carboxylic acid ester
Carboxamide group
Amino acid or derivatives
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboxylic acid
Carboxylic acid derivative
Carboximidic acid derivative
Carboximidic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Carbonyl group
Amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic 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	0.33	ALOGPS
logP	0.92	ChemAxon
logS	-4.3	ALOGPS
pKa (Strongest Acidic)	3.8	ChemAxon
pKa (Strongest Basic)	8.51	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	165.33 Å²	ChemAxon
Rotatable Bond Count	17	ChemAxon
Refractivity	149.63 m³·mol⁻¹	ChemAxon
Polarizability	61.12 Å³	ChemAxon
Number of Rings	2	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

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

163105109

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Detoxin D4 (NP0062013)

MOL for NP0062013 (Detoxin D4)

3D MOL for NP0062013 (Detoxin D4)

3D SDF for NP0062013 (Detoxin D4)

3D-SDF for NP0062013 (Detoxin D4)

PDB for NP0062013 (Detoxin D4)

3D PDB for NP0062013 (Detoxin D4)

SMILES for NP0062013 (Detoxin D4)

INCHI for NP0062013 (Detoxin D4)

Structure for NP0062013 (Detoxin D4)

3D Structure for NP0062013 (Detoxin D4)