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]deca-2,4-dienimidic acid (NP0291344)

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Record Information

Version

2.0

Created at

2022-09-09 22:23:51 UTC

Updated at

2022-09-09 22:23:52 UTC

NP-MRD ID

NP0291344

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]deca-2,4-dienimidic acid

Description

Glidobactin F 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 Glidobactin F.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309102200232D          

 35 35  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309102200232D          

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 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  1  0  0  0
 28 30  1  0  0  0  0
 30 31  2  0  0  0  0
 17 31  1  0  0  0  0
 31 32  1  4  0  0  0
 13 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0291344

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCC\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/C25H40N4O6/c1-4-5-6-7-8-9-10-11-22(33)29-23(18(3)30)25(35)28-20-16-19(31)14-15-26-21(32)13-12-17(2)27-24(20)34/h8-13,17-20,23,30-31H,4-7,14-16H2,1-3H3,(H,26,32)(H,27,34)(H,28,35)(H,29,33)/b9-8+,11-10+,13-12-/t17-,18+,19-,20-,23-/m0/s1

> <INCHI_KEY>
OJDBZOSAZHSDPV-UELYFCGDSA-N

> <FORMULA>
C25H40N4O6

> <MOLECULAR_WEIGHT>
492.617

> <EXACT_MASS>
492.294785024

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
54.00112968589443

> <JCHEM_BIOAVAILABILITY>
1

> <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]deca-2,4-dienimidic acid

> <JCHEM_LOGP>
-2.2181160665779647

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
-1.053109422902664

> <JCHEM_PKA_STRONGEST_ACIDIC>
-7.074805752396689

> <JCHEM_PKA_STRONGEST_BASIC>
15.328471885221223

> <JCHEM_POLAR_SURFACE_AREA>
170.82

> <JCHEM_REFRACTIVITY>
137.64220000000003

> <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]deca-2,4-dienimidic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-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      -6.668 -16.170   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.335 -15.400   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.001 -16.170   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.667 -15.400   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.334 -16.170   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.000 -15.400   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334 -16.170   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667 -15.400   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.667 -13.860   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0       4.001 -16.170   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       5.335 -15.400   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.668 -16.170   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       6.668 -17.710   0.000  0.00  0.00           O+0
HETATM   16  N   UNK     0       8.002 -15.400   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       9.336 -16.170   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.669 -15.400   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      10.669 -13.860   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       9.336 -13.090   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      12.003 -13.090   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      13.337 -13.860   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0      13.337 -15.400   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0      14.670 -16.170   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      16.004 -15.400   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      14.670 -17.710   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      13.337 -18.480   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      12.003 -17.710   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      12.003 -16.170   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0      10.669 -18.480   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0       9.336 -17.710   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       8.002 -18.480   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       5.335 -13.860   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.668 -13.090   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       4.001 -13.090   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    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   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   33                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18   31                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30   17   32                                                  
CONECT   32   31                                                            
CONECT   33   13   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₄₀N₄O₆

Average Mass

492.6170 Da

Monoisotopic Mass

492.29479 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]deca-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]deca-2,4-dienimidic acid

CAS Registry Number

Not Available

SMILES

CCCCC\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/C25H40N4O6/c1-4-5-6-7-8-9-10-11-22(33)29-23(18(3)30)25(35)28-20-16-19(31)14-15-26-21(32)13-12-17(2)27-24(20)34/h8-13,17-20,23,30-31H,4-7,14-16H2,1-3H3,(H,26,32)(H,27,34)(H,28,35)(H,29,33)/b9-8+,11-10+,13-12-/t17-,18+,19-,20-,23-/m0/s1

InChI Key

OJDBZOSAZHSDPV-UELYFCGDSA-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	-2.2	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	137.64 m³·mol⁻¹	ChemAxon
Polarizability	54 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	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

C00017641

Chemspider ID

4948094

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6444157

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]deca-2,4-dienimidic acid (NP0291344)

MOL for NP0291344 ((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]deca-2,4-dienimidic acid)

3D MOL for NP0291344 ((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]deca-2,4-dienimidic acid)

3D SDF for NP0291344 ((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]deca-2,4-dienimidic acid)

3D-SDF for NP0291344 ((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]deca-2,4-dienimidic acid)

PDB for NP0291344 ((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]deca-2,4-dienimidic acid)

3D PDB for NP0291344 ((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]deca-2,4-dienimidic acid)

SMILES for NP0291344 ((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]deca-2,4-dienimidic acid)

INCHI for NP0291344 ((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]deca-2,4-dienimidic acid)

Structure for NP0291344 ((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]deca-2,4-dienimidic acid)

3D Structure for NP0291344 ((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]deca-2,4-dienimidic acid)