NP-MRD: Showing NP-Card for 2-{[(1-{[(3z,9z)-2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6,9-tetraen-8-yl]-c-hydroxycarbonimidoyl}-2-methylpropyl)-c-hydroxycarbonimidoyl]amino}-3-methylpentanoic acid (NP0325332)

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Record Information

Version

1.0

Created at

2022-09-12 06:00:47 UTC

Updated at

2022-09-12 06:00:47 UTC

NP-MRD ID

NP0325332

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-{[(1-{[(3z,9z)-2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6,9-tetraen-8-yl]-c-hydroxycarbonimidoyl}-2-methylpropyl)-c-hydroxycarbonimidoyl]amino}-3-methylpentanoic acid

Description

Syringolin D belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone. 2-{[(1-{[(3z,9z)-2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6,9-tetraen-8-yl]-c-hydroxycarbonimidoyl}-2-methylpropyl)-c-hydroxycarbonimidoyl]amino}-3-methylpentanoic acid is found in Pseudomonas syringae. It was first documented in 2004 (PMID: 14714872). Based on a literature review very few articles have been published on Syringolin D.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122208002D          

 36 36  0  0  0  0            999 V2000
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   -0.6483   -6.8751    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


  Mrv1652309122208002D          

 36 36  0  0  0  0            999 V2000
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  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
  9 10  1  4  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
 13 14  1  4  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 19 18  1  4  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 28 24  1  4  0  0  0
 28 29  2  0  0  0  0
 14 29  1  0  0  0  0
 29 30  1  0  0  0  0
 10 31  1  0  0  0  0
 31 32  1  0  0  0  0
 31 33  1  0  0  0  0
  5 34  1  0  0  0  0
 34 35  2  0  0  0  0
 34 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0325332

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC(C)C(NC(O)=NC(C(C)C)C(O)=NC1\C=C/CCN=C(O)\C=C/C(N=C1O)C(C)C)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C25H41N5O6/c1-7-16(6)21(24(34)35)30-25(36)29-20(15(4)5)23(33)28-18-10-8-9-13-26-19(31)12-11-17(14(2)3)27-22(18)32/h8,10-12,14-18,20-21H,7,9,13H2,1-6H3,(H,26,31)(H,27,32)(H,28,33)(H,34,35)(H2,29,30,36)/b10-8-,12-11-

> <INCHI_KEY>
XQCDUALOSDLZKD-SIBMFBDYSA-N

> <FORMULA>
C25H41N5O6

> <MOLECULAR_WEIGHT>
507.632

> <EXACT_MASS>
507.30568406

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
77

> <JCHEM_AVERAGE_POLARIZABILITY>
53.954429078855505

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{[(1-{[(3Z,9Z)-2,7-dihydroxy-5-(propan-2-yl)-1,6-diazacyclododeca-1,3,6,9-tetraen-8-yl]-C-hydroxycarbonimidoyl}-2-methylpropyl)-C-hydroxycarbonimidoyl]amino}-3-methylpentanoic acid

> <JCHEM_LOGP>
-1.024444079609651

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
-0.27339776452446873

> <JCHEM_PKA_STRONGEST_ACIDIC>
-6.07383361719426

> <JCHEM_PKA_STRONGEST_BASIC>
15.361193793684604

> <JCHEM_POLAR_SURFACE_AREA>
179.69

> <JCHEM_REFRACTIVITY>
137.75590000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
2-{[(1-{[(3Z,9Z)-2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6,9-tetraen-8-yl]-C-hydroxycarbonimidoyl}-2-methylpropyl)-C-hydroxycarbonimidoyl]amino}-3-methylpentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0      -5.211  -7.443   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.878  -8.213   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.878  -9.753   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.211 -10.523   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.544 -10.523   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -2.544 -12.063   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -1.210 -12.833   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       0.123 -12.063   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0      -1.210 -14.373   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       0.123 -15.143   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.123 -16.683   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       1.457 -17.453   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0      -1.210 -17.453   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      -1.210 -18.993   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.277 -19.392   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.366 -20.481   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.765 -21.969   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.366 -23.456   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       0.277 -24.545   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0      -1.210 -24.944   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -1.210 -26.484   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -2.698 -24.545   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -3.787 -23.456   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -4.185 -21.969   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -5.725 -21.969   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -6.495 -20.635   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -6.495 -23.302   0.000  0.00  0.00           C+0
HETATM   28  N   UNK     0      -3.787 -20.481   0.000  0.00  0.00           N+0
HETATM   29  C   UNK     0      -2.698 -19.392   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -3.468 -18.058   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       1.457 -14.373   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.791 -15.143   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       1.457 -12.833   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -1.210  -9.753   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -1.210  -8.213   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       0.123 -10.523   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   34                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   31                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   29                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   28                                                  
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25                                                            
CONECT   28   24   29                                                       
CONECT   29   28   14   30                                                  
CONECT   30   29                                                            
CONECT   31   10   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31                                                            
CONECT   34    5   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

C₂₅H₄₁N₅O₆

Average Mass

507.6320 Da

Monoisotopic Mass

507.30568 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CCC(C)C(NC(O)=NC(C(C)C)C(O)=NC1\C=C/CCN=C(O)\C=C/C(N=C1O)C(C)C)C(O)=O

InChI Identifier

InChI=1S/C25H41N5O6/c1-7-16(6)21(24(34)35)30-25(36)29-20(15(4)5)23(33)28-18-10-8-9-13-26-19(31)12-11-17(14(2)3)27-22(18)32/h8,10-12,14-18,20-21H,7,9,13H2,1-6H3,(H,26,31)(H,27,32)(H,28,33)(H,34,35)(H2,29,30,36)/b10-8-,12-11-

InChI Key

XQCDUALOSDLZKD-SIBMFBDYSA-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
Pseudomonas syringae	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Cyclic peptides

Alternative Parents

Substituents

Cyclic alpha peptide
Isoleucine or derivatives
Alpha-amino acid or derivatives
Methyl-branched fatty acid
Heterocyclic fatty acid
Branched fatty acid
Fatty acyl
Cyclic carboximidic acid
Isourea
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboximidamide
Monocarboxylic acid or derivatives
Carboxylic acid
Carboximidic acid derivative
Carboximidic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
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

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

78443977

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139584262

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Amrein H, Makart S, Granado J, Shakya R, Schneider-Pokorny J, Dudler R: Functional analysis of genes involved in the synthesis of syringolin A by Pseudomonas syringae pv. syringae B301 D-R. Mol Plant Microbe Interact. 2004 Jan;17(1):90-7. doi: 10.1094/MPMI.2004.17.1.90. [PubMed:14714872 ]
LOTUS database [Link]

Showing NP-Card for 2-{[(1-{[(3z,9z)-2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6,9-tetraen-8-yl]-c-hydroxycarbonimidoyl}-2-methylpropyl)-c-hydroxycarbonimidoyl]amino}-3-methylpentanoic acid (NP0325332)

MOL for NP0325332 (2-{[(1-{[(3z,9z)-2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6,9-tetraen-8-yl]-c-hydroxycarbonimidoyl}-2-methylpropyl)-c-hydroxycarbonimidoyl]amino}-3-methylpentanoic acid)

3D MOL for NP0325332 (2-{[(1-{[(3z,9z)-2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6,9-tetraen-8-yl]-c-hydroxycarbonimidoyl}-2-methylpropyl)-c-hydroxycarbonimidoyl]amino}-3-methylpentanoic acid)

3D SDF for NP0325332 (2-{[(1-{[(3z,9z)-2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6,9-tetraen-8-yl]-c-hydroxycarbonimidoyl}-2-methylpropyl)-c-hydroxycarbonimidoyl]amino}-3-methylpentanoic acid)

3D-SDF for NP0325332 (2-{[(1-{[(3z,9z)-2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6,9-tetraen-8-yl]-c-hydroxycarbonimidoyl}-2-methylpropyl)-c-hydroxycarbonimidoyl]amino}-3-methylpentanoic acid)

PDB for NP0325332 (2-{[(1-{[(3z,9z)-2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6,9-tetraen-8-yl]-c-hydroxycarbonimidoyl}-2-methylpropyl)-c-hydroxycarbonimidoyl]amino}-3-methylpentanoic acid)

3D PDB for NP0325332 (2-{[(1-{[(3z,9z)-2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6,9-tetraen-8-yl]-c-hydroxycarbonimidoyl}-2-methylpropyl)-c-hydroxycarbonimidoyl]amino}-3-methylpentanoic acid)

SMILES for NP0325332 (2-{[(1-{[(3z,9z)-2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6,9-tetraen-8-yl]-c-hydroxycarbonimidoyl}-2-methylpropyl)-c-hydroxycarbonimidoyl]amino}-3-methylpentanoic acid)

INCHI for NP0325332 (2-{[(1-{[(3z,9z)-2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6,9-tetraen-8-yl]-c-hydroxycarbonimidoyl}-2-methylpropyl)-c-hydroxycarbonimidoyl]amino}-3-methylpentanoic acid)

Structure for NP0325332 (2-{[(1-{[(3z,9z)-2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6,9-tetraen-8-yl]-c-hydroxycarbonimidoyl}-2-methylpropyl)-c-hydroxycarbonimidoyl]amino}-3-methylpentanoic acid)

3D Structure for NP0325332 (2-{[(1-{[(3z,9z)-2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6,9-tetraen-8-yl]-c-hydroxycarbonimidoyl}-2-methylpropyl)-c-hydroxycarbonimidoyl]amino}-3-methylpentanoic acid)