NP-MRD: Showing NP-Card for (3r,9r)-3,9-diamino-1,7-diazacyclododeca-1,7-diene-2,8-diol (NP0170157)

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Record Information

Version

2.0

Created at

2022-09-03 06:15:35 UTC

Updated at

2022-09-03 06:15:35 UTC

NP-MRD ID

NP0170157

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3r,9r)-3,9-diamino-1,7-diazacyclododeca-1,7-diene-2,8-diol

Description

(3R,9R)-3,9-Diamino-1,7-diazacyclododecane-2,8-dione belongs to the class of organic compounds known as macrolactams. These are cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. They are nitrogen analogues (the a nitrogen atom replacing the o atom of the cyclic carboxylic acid group ) of the naturally occurring macrolides. (3r,9r)-3,9-diamino-1,7-diazacyclododeca-1,7-diene-2,8-diol is found in Protohermes grandis. Based on a literature review very few articles have been published on (3R,9R)-3,9-Diamino-1,7-diazacyclododecane-2,8-dione.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 36  0  0  0  0  0  0  0  0999 V2000
    3.6801   -0.7558   -0.9352 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2400   -0.5922   -0.6437 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1416    0.6326    0.2383 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1335    1.6540   -0.3096 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3405    2.2882    0.8104 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0058    2.5256    0.6004 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0568    1.9726    0.2494 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2770    2.6958    0.1881 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1348    0.5574   -0.1256 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5349    0.1203   -0.3047 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5356   -0.4211    0.8167 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6036   -1.7883    0.1142 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3602   -1.9329   -0.7781 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7337   -2.2963    0.0671 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8670   -1.7582    0.1651 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7912   -2.2699    1.0536 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1573   -0.6870   -0.0087 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8207   -1.7486   -1.2573 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6838   -0.4645   -1.5773 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1360    1.1130    0.4184 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7768    0.3748    1.2567 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7964    2.4202   -0.8203 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5326    1.2362   -1.1200 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8336    3.3097    0.9900 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6155    1.7423    1.7428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5568    2.9393   -0.7617 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6620    0.3832   -1.1398 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0275    0.2155    0.6092 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9530    0.8454   -0.9426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2132   -0.5395    1.7104 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5376   -0.2248    1.1854 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4723   -1.8435   -0.5728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6651   -2.6154    0.8210 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5506   -2.8263   -1.4407 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2157   -1.0251   -1.3816 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0826   -3.2368    1.0821 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 15  2  1  0
  1 17  1  0
  1 18  1  0
  2 19  1  6
  3 20  1  0
  3 21  1  0
  4 22  1  0
  4 23  1  0
  5 24  1  0
  5 25  1  0
  8 26  1  0
  9 27  1  6
 10 28  1  0
 10 29  1  0
 11 30  1  0
 11 31  1  0
 12 32  1  0
 12 33  1  0
 13 34  1  0
 13 35  1  0
 16 36  1  0
M  END


  Mrv1652309032208152D          

 16 16  0  0  1  0            999 V2000
    1.4289    1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  2  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
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 N   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
    2.8579   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  6  5  1  4  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  6  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 14 13  1  4  0  0  0
 14 15  2  0  0  0  0
  2 15  1  0  0  0  0
 15 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0170157

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N[C@@H]1CCCN=C(O)[C@H](N)CCCN=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C10H20N4O2/c11-7-3-1-5-13-10(16)8(12)4-2-6-14-9(7)15/h7-8H,1-6,11-12H2,(H,13,16)(H,14,15)/t7-,8-/m1/s1

> <INCHI_KEY>
NWDFWCXKIDTJBA-HTQZYQBOSA-N

> <FORMULA>
C10H20N4O2

> <MOLECULAR_WEIGHT>
228.296

> <EXACT_MASS>
228.1586259

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
24.648046580074265

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,9R)-3,9-diamino-1,7-diazacyclododeca-1,7-diene-2,8-diol

> <ALOGPS_LOGP>
-0.79

> <JCHEM_LOGP>
-5.8777905304353615

> <ALOGPS_LOGS>
-2.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
-2.3012239345604426

> <JCHEM_PKA_STRONGEST_ACIDIC>
-5.3250515487873455

> <JCHEM_PKA_STRONGEST_BASIC>
15.301031774171907

> <JCHEM_POLAR_SURFACE_AREA>
117.22

> <JCHEM_REFRACTIVITY>
61.06060000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.10e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R,9R)-3,9-diamino-1,7-diazacyclododeca-1,7-diene-2,8-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  N   UNK     0       2.667   3.080   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       4.001  -0.770   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       2.667  -4.620   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      -0.000   1.540   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   15                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14    2   16                                                  
CONECT   16   15                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₂₀N₄O₂

Average Mass

228.2960 Da

Monoisotopic Mass

228.15863 Da

IUPAC Name

(3R,9R)-3,9-diamino-1,7-diazacyclododeca-1,7-diene-2,8-diol

Traditional Name

(3R,9R)-3,9-diamino-1,7-diazacyclododeca-1,7-diene-2,8-diol

CAS Registry Number

Not Available

SMILES

N[C@@H]1CCCN=C(O)[C@H](N)CCCN=C1O

InChI Identifier

InChI=1S/C10H20N4O2/c11-7-3-1-5-13-10(16)8(12)4-2-6-14-9(7)15/h7-8H,1-6,11-12H2,(H,13,16)(H,14,15)/t7-,8-/m1/s1

InChI Key

NWDFWCXKIDTJBA-HTQZYQBOSA-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
Protohermes grandis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as macrolactams. These are cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. They are nitrogen analogues (the a nitrogen atom replacing the o atom of the cyclic carboxylic acid group ) of the naturally occurring macrolides.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Macrolactams

Sub Class

Not Available

Direct Parent

Macrolactams

Alternative Parents

Substituents

Macrolactam
Alpha-amino acid amide
Alpha-amino acid or derivatives
Amino acid or derivatives
Carboxamide group
Secondary carboxylic acid amide
Lactam
Azacycle
Organoheterocyclic compound
Carboxylic acid derivative
Organic nitrogen compound
Primary aliphatic amine
Organonitrogen compound
Organooxygen compound
Primary amine
Hydrocarbon derivative
Carbonyl group
Organic oxide
Amine
Organic oxygen 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	-0.79	ALOGPS
logP	-5.9	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	-5.3	ChemAxon
pKa (Strongest Basic)	15.3	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	117.22 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	61.06 m³·mol⁻¹	ChemAxon
Polarizability	24.65 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

28286543

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101477400

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3r,9r)-3,9-diamino-1,7-diazacyclododeca-1,7-diene-2,8-diol (NP0170157)

MOL for NP0170157 ((3r,9r)-3,9-diamino-1,7-diazacyclododeca-1,7-diene-2,8-diol)

3D MOL for NP0170157 ((3r,9r)-3,9-diamino-1,7-diazacyclododeca-1,7-diene-2,8-diol)

3D SDF for NP0170157 ((3r,9r)-3,9-diamino-1,7-diazacyclododeca-1,7-diene-2,8-diol)

3D-SDF for NP0170157 ((3r,9r)-3,9-diamino-1,7-diazacyclododeca-1,7-diene-2,8-diol)

PDB for NP0170157 ((3r,9r)-3,9-diamino-1,7-diazacyclododeca-1,7-diene-2,8-diol)

3D PDB for NP0170157 ((3r,9r)-3,9-diamino-1,7-diazacyclododeca-1,7-diene-2,8-diol)

SMILES for NP0170157 ((3r,9r)-3,9-diamino-1,7-diazacyclododeca-1,7-diene-2,8-diol)

INCHI for NP0170157 ((3r,9r)-3,9-diamino-1,7-diazacyclododeca-1,7-diene-2,8-diol)

Structure for NP0170157 ((3r,9r)-3,9-diamino-1,7-diazacyclododeca-1,7-diene-2,8-diol)

3D Structure for NP0170157 ((3r,9r)-3,9-diamino-1,7-diazacyclododeca-1,7-diene-2,8-diol)