NP-MRD: Showing NP-Card for 2-[({1-[(2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6-trien-8-yl)-c-hydroxycarbonimidoyl]-2-methylpropyl}-c-hydroxycarbonimidoyl)amino]-3-methylbutanoic acid (NP0153845)

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Record Information

Version

2.0

Created at

2022-09-02 10:34:24 UTC

Updated at

2022-09-02 10:34:25 UTC

NP-MRD ID

NP0153845

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

N-{[(1S)-2-methyl-1-{[(5S,8S)-5-(1-methylethyl)-2,7-dioxo-1,6-diazacyclododec-3-en-8-yl]carbamoyl}propyl]carbamoyl}-L-valine 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-[(2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6-trien-8-yl)-c-hydroxycarbonimidoyl]-2-methylpropyl}-c-hydroxycarbonimidoyl)amino]-3-methylbutanoic acid is found in Pseudomonas syringae. Based on a literature review very few articles have been published on N-{[(1S)-2-methyl-1-{[(5S,8S)-5-(1-methylethyl)-2,7-dioxo-1,6-diazacyclododec-3-en-8-yl]carbamoyl}propyl]carbamoyl}-L-valine.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309022212342D          

 35 35  0  0  0  0            999 V2000
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M  END

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M  END


  Mrv1652309022212342D          

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  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
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 15 14  1  4  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 16 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  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 24 26  1  0  0  0  0
 23 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 18 30  1  0  0  0  0
 30 31  1  0  0  0  0
 30 32  1  0  0  0  0
 14 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  2  0  0  0  0
 35  4  1  4  0  0  0
M  END
> <DATABASE_ID>
NP0153845

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)C(NC(O)=NC(C(C)C)C(O)=NC1CCCCN=C(O)C=CC(N=C1O)C(C)C)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C24H41N5O6/c1-13(2)16-10-11-18(30)25-12-8-7-9-17(21(31)26-16)27-22(32)19(14(3)4)28-24(35)29-20(15(5)6)23(33)34/h10-11,13-17,19-20H,7-9,12H2,1-6H3,(H,25,30)(H,26,31)(H,27,32)(H,33,34)(H2,28,29,35)

> <INCHI_KEY>
AIMDTYKFJMYVNG-UHFFFAOYSA-N

> <FORMULA>
C24H41N5O6

> <MOLECULAR_WEIGHT>
495.621

> <EXACT_MASS>
495.30568406

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
53.33067988692245

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
1.80

> <JCHEM_LOGP>
-1.226024685211061

> <ALOGPS_LOGS>
-4.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
-0.16188794769033787

> <JCHEM_PKA_STRONGEST_ACIDIC>
-5.664411023446447

> <JCHEM_PKA_STRONGEST_BASIC>
15.36129521042814

> <JCHEM_POLAR_SURFACE_AREA>
179.69

> <JCHEM_REFRACTIVITY>
132.19230000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.61e-02 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       6.668  -0.770   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0       4.001  -0.770   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      -1.334  -0.770   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0      -4.001  -2.310   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   22  N   UNK     0      -5.335  -4.620   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -5.335  -7.700   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -0.000   1.540   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   35  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   35                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   33                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19   30                                                  
CONECT   19   18   20                                                       
CONECT   20   19   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                                                            
CONECT   30   18   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30                                                            
CONECT   33   14   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33    4                                                       
MASTER        0    0    0    0    0    0    0    0   35    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₄₁N₅O₆

Average Mass

495.6210 Da

Monoisotopic Mass

495.30568 Da

IUPAC Name

2-{[(1-{[2,7-dihydroxy-5-(propan-2-yl)-1,6-diazacyclododeca-1,3,6-trien-8-yl]-C-hydroxycarbonimidoyl}-2-methylpropyl)-C-hydroxycarbonimidoyl]amino}-3-methylbutanoic acid

Traditional Name

2-[({1-[(2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6-trien-8-yl)-C-hydroxycarbonimidoyl]-2-methylpropyl}-C-hydroxycarbonimidoyl)amino]-3-methylbutanoic acid

CAS Registry Number

Not Available

SMILES

CC(C)C(NC(O)=NC(C(C)C)C(O)=NC1CCCCN=C(O)C=CC(N=C1O)C(C)C)C(O)=O

InChI Identifier

InChI=1S/C24H41N5O6/c1-13(2)16-10-11-18(30)25-12-8-7-9-17(21(31)26-16)27-22(32)19(14(3)4)28-24(35)29-20(15(5)6)23(33)34/h10-11,13-17,19-20H,7-9,12H2,1-6H3,(H,25,30)(H,26,31)(H,27,32)(H,33,34)(H2,28,29,35)

InChI Key

AIMDTYKFJMYVNG-UHFFFAOYSA-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
Valine or derivatives
Alpha-amino acid or derivatives
Branched fatty acid
Heterocyclic fatty acid
Methyl-branched fatty acid
Fatty acyl
Cyclic carboximidic acid
Isourea
Carboximidic acid
Carboximidic acid derivative
Carboxylic acid
Azacycle
Monocarboxylic acid or derivatives
Carboximidamide
Organoheterocyclic compound
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Carbonyl group
Organonitrogen compound
Organooxygen compound
Organic nitrogen compound
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
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	1.8	ALOGPS
logP	-1.2	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Acidic)	-5.7	ChemAxon
pKa (Strongest Basic)	15.36	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	179.69 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	132.19 m³·mol⁻¹	ChemAxon
Polarizability	53.33 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

Not Available

Chemspider ID

28537598

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

75083844

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2-[({1-[(2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6-trien-8-yl)-c-hydroxycarbonimidoyl]-2-methylpropyl}-c-hydroxycarbonimidoyl)amino]-3-methylbutanoic acid (NP0153845)

MOL for NP0153845 (2-[({1-[(2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6-trien-8-yl)-c-hydroxycarbonimidoyl]-2-methylpropyl}-c-hydroxycarbonimidoyl)amino]-3-methylbutanoic acid)

3D MOL for NP0153845 (2-[({1-[(2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6-trien-8-yl)-c-hydroxycarbonimidoyl]-2-methylpropyl}-c-hydroxycarbonimidoyl)amino]-3-methylbutanoic acid)

3D SDF for NP0153845 (2-[({1-[(2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6-trien-8-yl)-c-hydroxycarbonimidoyl]-2-methylpropyl}-c-hydroxycarbonimidoyl)amino]-3-methylbutanoic acid)

3D-SDF for NP0153845 (2-[({1-[(2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6-trien-8-yl)-c-hydroxycarbonimidoyl]-2-methylpropyl}-c-hydroxycarbonimidoyl)amino]-3-methylbutanoic acid)

PDB for NP0153845 (2-[({1-[(2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6-trien-8-yl)-c-hydroxycarbonimidoyl]-2-methylpropyl}-c-hydroxycarbonimidoyl)amino]-3-methylbutanoic acid)

3D PDB for NP0153845 (2-[({1-[(2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6-trien-8-yl)-c-hydroxycarbonimidoyl]-2-methylpropyl}-c-hydroxycarbonimidoyl)amino]-3-methylbutanoic acid)

SMILES for NP0153845 (2-[({1-[(2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6-trien-8-yl)-c-hydroxycarbonimidoyl]-2-methylpropyl}-c-hydroxycarbonimidoyl)amino]-3-methylbutanoic acid)

INCHI for NP0153845 (2-[({1-[(2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6-trien-8-yl)-c-hydroxycarbonimidoyl]-2-methylpropyl}-c-hydroxycarbonimidoyl)amino]-3-methylbutanoic acid)

Structure for NP0153845 (2-[({1-[(2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6-trien-8-yl)-c-hydroxycarbonimidoyl]-2-methylpropyl}-c-hydroxycarbonimidoyl)amino]-3-methylbutanoic acid)

3D Structure for NP0153845 (2-[({1-[(2,7-dihydroxy-5-isopropyl-1,6-diazacyclododeca-1,3,6-trien-8-yl)-c-hydroxycarbonimidoyl]-2-methylpropyl}-c-hydroxycarbonimidoyl)amino]-3-methylbutanoic acid)