NP-MRD: Showing NP-Card for Pseudotheonamide D (NP0070351)

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Record Information

Version

2.0

Created at

2022-04-28 15:43:37 UTC

Updated at

2022-04-28 15:43:37 UTC

NP-MRD ID

NP0070351

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pseudotheonamide D

Description

(2S)-1-[(2S)-3-{[(2E,4S)-4-{[(2R)-2-amino-1-hydroxy-3-phenylpropylidene]amino}-1-hydroxy-5-(4-hydroxyphenyl)pent-2-en-1-ylidene]amino}-2-[(hydroxymethylidene)amino]propanoyl]pyrrolidine-2-carboximidic acid 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. Pseudotheonamide D is found in Theonella swinhoei. Based on a literature review very few articles have been published on (2S)-1-[(2S)-3-{[(2E,4S)-4-{[(2R)-2-amino-1-hydroxy-3-phenylpropylidene]amino}-1-hydroxy-5-(4-hydroxyphenyl)pent-2-en-1-ylidene]amino}-2-[(hydroxymethylidene)amino]propanoyl]pyrrolidine-2-carboximidic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282217432D          

 41 43  0  0  1  0            999 V2000
    6.4694   -7.0894    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0215   -7.7025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.8020   -8.2455    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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    5.0013   -7.0125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -7.4250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    3.5724   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
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  8 36  1  6  0  0  0
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 37 38  2  0  0  0  0
  4 39  1  1  0  0  0
 39 40  2  0  0  0  0
 39 41  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304282217432D          

 41 43  0  0  1  0            999 V2000
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    7.1447    1.6500    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
    7.8592    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -5.7750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1889   -8.7975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3604   -9.6045    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4043   -8.5426    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 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
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 17 22  1  0  0  0  0
 20 23  1  0  0  0  0
 15 24  1  6  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 29 34  1  0  0  0  0
 27 35  1  1  0  0  0
  8 36  1  6  0  0  0
 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
  4 39  1  1  0  0  0
 39 40  2  0  0  0  0
 39 41  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0070351

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N[C@H](CC1=CC=CC=C1)C(=O)N[C@@H](CC1=CC=C(O)C=C1)\C=C\C(=O)NC[C@H](NC=O)C(=O)N1CCC[C@H]1C(N)=O

> <INCHI_IDENTIFIER>
InChI=1S/C29H36N6O6/c30-23(16-19-5-2-1-3-6-19)28(40)34-21(15-20-8-11-22(37)12-9-20)10-13-26(38)32-17-24(33-18-36)29(41)35-14-4-7-25(35)27(31)39/h1-3,5-6,8-13,18,21,23-25,37H,4,7,14-17,30H2,(H2,31,39)(H,32,38)(H,33,36)(H,34,40)/b13-10+/t21-,23-,24+,25+/m1/s1

> <INCHI_KEY>
RCIDYXROFLLKED-GBUQLMHESA-N

> <FORMULA>
C29H36N6O6

> <MOLECULAR_WEIGHT>
564.643

> <EXACT_MASS>
564.269632903

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
77

> <JCHEM_AVERAGE_POLARIZABILITY>
59.29263802856889

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-1-[(2S)-3-[(2E,4S)-4-[(2R)-2-amino-3-phenylpropanamido]-5-(4-hydroxyphenyl)pent-2-enamido]-2-formamidopropanoyl]pyrrolidine-2-carboxamide

> <ALOGPS_LOGP>
0.46

> <JCHEM_LOGP>
-0.7282879706845753

> <ALOGPS_LOGS>
-4.25

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.45933302595639

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.517211332911277

> <JCHEM_PKA_STRONGEST_BASIC>
7.995166734762715

> <JCHEM_POLAR_SURFACE_AREA>
196.95

> <JCHEM_REFRACTIVITY>
151.59280000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.16e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-1-[(2S)-3-[(2E,4S)-4-[(2R)-2-amino-3-phenylpropanamido]-5-(4-hydroxyphenyl)pent-2-enamido]-2-formamidopropanoyl]pyrrolidine-2-carboxamide

> <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      12.076 -13.234   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.107 -14.378   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      12.337 -15.712   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.830 -15.392   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      10.669 -13.860   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       9.336 -13.090   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       8.002 -13.860   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       9.336 -11.550   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.002 -10.780   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       8.002  -9.240   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       6.668  -8.470   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.335  -9.240   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.002  -6.160   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.668  -3.850   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.335  -6.160   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.667  -6.160   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.001  -3.850   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   24  N   UNK     0       9.336  -3.850   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       8.002  -1.540   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      10.669  -1.540   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      10.669   0.000   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      12.003   0.770   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      12.003   2.310   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      13.337   3.080   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      14.670   2.310   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      14.670   0.770   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      13.337   0.000   0.000  0.00  0.00           C+0
HETATM   35  N   UNK     0      12.003  -2.310   0.000  0.00  0.00           N+0
HETATM   36  N   UNK     0      10.669 -10.780   0.000  0.00  0.00           N+0
HETATM   37  C   UNK     0      10.669  -9.240   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       9.336  -8.470   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0       9.686 -16.422   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0      10.006 -17.928   0.000  0.00  0.00           O+0
HETATM   41  N   UNK     0       8.221 -15.946   0.000  0.00  0.00           N+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   39                                                  
CONECT    5    4    1    6                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   36                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   24                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   22                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   23                                                  
CONECT   21   20   22                                                       
CONECT   22   21   17                                                       
CONECT   23   20                                                            
CONECT   24   15   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   35                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   34                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   29                                                       
CONECT   35   27                                                            
CONECT   36    8   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37                                                            
CONECT   39    4   40   41                                                  
CONECT   40   39                                                            
CONECT   41   39                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   86    0
END

View in JSmol

Synonyms

Value	Source
(2S)-1-[(2S)-3-{[(2E,4S)-4-{[(2R)-2-amino-1-hydroxy-3-phenylpropylidene]amino}-1-hydroxy-5-(4-hydroxyphenyl)pent-2-en-1-ylidene]amino}-2-[(hydroxymethylidene)amino]propanoyl]pyrrolidine-2-carboximidate	Generator

Chemical Formula

C₂₉H₃₆N₆O₆

Average Mass

564.6430 Da

Monoisotopic Mass

564.26963 Da

IUPAC Name

(2S)-1-[(2S)-3-[(2E,4S)-4-[(2R)-2-amino-3-phenylpropanamido]-5-(4-hydroxyphenyl)pent-2-enamido]-2-formamidopropanoyl]pyrrolidine-2-carboxamide

Traditional Name

(2S)-1-[(2S)-3-[(2E,4S)-4-[(2R)-2-amino-3-phenylpropanamido]-5-(4-hydroxyphenyl)pent-2-enamido]-2-formamidopropanoyl]pyrrolidine-2-carboxamide

CAS Registry Number

Not Available

SMILES

N[C@H](CC1=CC=CC=C1)C(=O)N[C@@H](CC1=CC=C(O)C=C1)\C=C\C(=O)NC[C@H](NC=O)C(=O)N1CCC[C@H]1C(N)=O

InChI Identifier

InChI=1S/C29H36N6O6/c30-23(16-19-5-2-1-3-6-19)28(40)34-21(15-20-8-11-22(37)12-9-20)10-13-26(38)32-17-24(33-18-36)29(41)35-14-4-7-25(35)27(31)39/h1-3,5-6,8-13,18,21,23-25,37H,4,7,14-17,30H2,(H2,31,39)(H,32,38)(H,33,36)(H,34,40)/b13-10+/t21-,23-,24+,25+/m1/s1

InChI Key

RCIDYXROFLLKED-GBUQLMHESA-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
Theonella swinhoei	-	KNApSAcK

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
Phenylalanine or derivatives
Proline or derivatives
Alpha-amino acid amide
N-formyl-alpha amino acid or derivatives
N-formyl-alpha-amino acid
Beta amino acid or derivatives
Alpha-amino acid or derivatives
Amphetamine or derivatives
N-acylpyrrolidine
Pyrrolidine carboxylic acid or derivatives
Pyrrolidine-2-carboxamide
Phenol
1-hydroxy-2-unsubstituted benzenoid
Aralkylamine
Benzenoid
N-acyl-amine
Monocyclic benzene moiety
Fatty amide
Fatty acyl
Tertiary carboxylic acid amide
Pyrrolidine
Amino acid or derivatives
Carboxamide group
Secondary carboxylic acid amide
Primary carboxylic acid amide
Organoheterocyclic compound
Azacycle
Amine
Primary aliphatic amine
Organic oxygen compound
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organic nitrogen compound
Primary amine
Organooxygen compound
Organonitrogen compound
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	0.46	ALOGPS
logP	-0.73	ChemAxon
logS	-4.2	ALOGPS
pKa (Strongest Acidic)	9.52	ChemAxon
pKa (Strongest Basic)	8	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	196.95 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	151.59 m³·mol⁻¹	ChemAxon
Polarizability	59.29 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

8873525

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10698183

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Pseudotheonamide D (NP0070351)

MOL for NP0070351 (Pseudotheonamide D)

3D MOL for NP0070351 (Pseudotheonamide D)

3D SDF for NP0070351 (Pseudotheonamide D)

3D-SDF for NP0070351 (Pseudotheonamide D)

PDB for NP0070351 (Pseudotheonamide D)

3D PDB for NP0070351 (Pseudotheonamide D)

SMILES for NP0070351 (Pseudotheonamide D)

INCHI for NP0070351 (Pseudotheonamide D)

Structure for NP0070351 (Pseudotheonamide D)

3D Structure for NP0070351 (Pseudotheonamide D)