NP-MRD: Showing NP-Card for (e)-5,5'-diamino-2,2'-dihydroxy-[3,3'-bipyridinylidene]-6,6'-dione (NP0211757)

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Record Information

Version

2.0

Created at

2022-09-05 10:10:31 UTC

Updated at

2022-09-05 10:10:32 UTC

NP-MRD ID

NP0211757

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(e)-5,5'-diamino-2,2'-dihydroxy-[3,3'-bipyridinylidene]-6,6'-dione

Description

Indigoidine belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. Indigoidine is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. (e)-5,5'-diamino-2,2'-dihydroxy-[3,3'-bipyridinylidene]-6,6'-dione is found in Streptomyces chromofuscus. (e)-5,5'-diamino-2,2'-dihydroxy-[3,3'-bipyridinylidene]-6,6'-dione was first documented in 2022 (PMID: 35819797). Based on a literature review a small amount of articles have been published on indigoidine (PMID: 35771110) (PMID: 35737654) (PMID: 35471079) (PMID: 35456738).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052212102D          

 18 19  0  0  0  0            999 V2000
    2.1434    2.0625    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    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
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  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  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
  5 12  1  0  0  0  0
 12 13  1  0  0  0  0
  4 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
 16 17  1  0  0  0  0
  2 17  1  0  0  0  0
 17 18  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0211757

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=C\C(C(O)=NC1=O)=C1\C=C(N)C(=O)N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C10H8N4O4/c11-5-1-3(7(15)13-9(5)17)4-2-6(12)10(18)14-8(4)16/h1-2H,11-12H2,(H,13,15,17)(H,14,16,18)/b4-3+

> <INCHI_KEY>
ALDIVIWLBSDGGN-ONEGZZNKSA-N

> <FORMULA>
C10H8N4O4

> <MOLECULAR_WEIGHT>
248.198

> <EXACT_MASS>
248.054554754

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
22.157269188080864

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(E)-5,5'-diamino-2,2'-dihydroxy-6H,6'H-[3,3'-bipyridinylidene]-6,6'-dione

> <JCHEM_LOGP>
-2.8830280066666663

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
3.339216823384638

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.4088062281589524

> <JCHEM_PKA_STRONGEST_BASIC>
0.5329622247077372

> <JCHEM_POLAR_SURFACE_AREA>
151.36

> <JCHEM_REFRACTIVITY>
62.624600000000015

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(E)-5,5'-diamino-2,2'-dihydroxy-[3,3'-bipyridinylidene]-6,6'-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  N   UNK     0       4.001   3.850   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       8.002  -4.620   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      10.669  -3.080   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0       9.336  -0.770   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       8.002   1.540   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   16  N   UNK     0       2.667   0.000   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   17                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   14                                                  
CONECT    5    4    6   12                                                  
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    5   13                                                  
CONECT   13   12                                                            
CONECT   14    4   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16    2   18                                                  
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

View in JSmol

Synonyms

Value	Source
5,5'-Diamino-4,4'-dihydroxy-3,3'-diazadiphenoquinone-(2,2')	ChEBI

Chemical Formula

C₁₀H₈N₄O₄

Average Mass

248.1980 Da

Monoisotopic Mass

248.05455 Da

IUPAC Name

(E)-5,5'-diamino-2,2'-dihydroxy-6H,6'H-[3,3'-bipyridinylidene]-6,6'-dione

Traditional Name

(E)-5,5'-diamino-2,2'-dihydroxy-[3,3'-bipyridinylidene]-6,6'-dione

CAS Registry Number

Not Available

SMILES

NC1=C\C(C(O)=NC1=O)=C1\C=C(N)C(=O)N=C1O

InChI Identifier

InChI=1S/C10H8N4O4/c11-5-1-3(7(15)13-9(5)17)4-2-6(12)10(18)14-8(4)16/h1-2H,11-12H2,(H,13,15,17)(H,14,16,18)/b4-3+

InChI Key

ALDIVIWLBSDGGN-ONEGZZNKSA-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
Streptomyces chromofuscus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
Hydropyridine
Carboxylic acid imide
Dicarboximide
Carboxylic acid imide, n-unsubstituted
Enamine
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Primary amine
Primary aliphatic amine
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Amine
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

dicarboximide (CHEBI:79296 )
enamine (CHEBI:79296 )
ring assembly (CHEBI:79296 )
pyridone (CHEBI:79296 )

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	-2.9	ChemAxon
pKa (Strongest Acidic)	2.41	ChemAxon
pKa (Strongest Basic)	0.53	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	151.36 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	62.62 m³·mol⁻¹	ChemAxon
Polarizability	22.16 Å³	ChemAxon
Number of Rings	2	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

4590923

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5492261

PDB ID

Not Available

ChEBI ID

79296

Good Scents ID

Not Available

References

General References

Chen S, Hu M, Hu A, Xue Y, Wang S, Liu F, Li C, Zhou X, Zhou J: The integration host factor regulates multiple virulence pathways in bacterial pathogen Dickeya zeae MS2. Mol Plant Pathol. 2022 Oct;23(10):1487-1507. doi: 10.1111/mpp.13244. Epub 2022 Jul 12. [PubMed:35819797 ]
Wu YM, Wang LH, Chu CC: First report of Dickeya dadantii causing bacterial soft rot of Thaumatophyllum bipinnatifidum in Taiwan. Plant Dis. 2022 Jun 30. doi: 10.1094/PDIS-04-22-0924-PDN. [PubMed:35771110 ]
Panchanawaporn S, Chutrakul C, Jeennor S, Anantayanon J, Rattanaphan N, Laoteng K: Potential of Aspergillus oryzae as a biosynthetic platform for indigoidine, a non-ribosomal peptide pigment with antioxidant activity. PLoS One. 2022 Jun 23;17(6):e0270359. doi: 10.1371/journal.pone.0270359. eCollection 2022. [PubMed:35737654 ]
Wang LH, Tang WQ, Chan JJ, Lee YJ, Chang CY, Fang ZQ, Chu CC: First report of bacterial soft rot on Epipremnum aureum caused by Pectobacterium aroidearum in Taiwan. Plant Dis. 2022 Apr 26. doi: 10.1094/PDIS-03-22-0578-PDN. [PubMed:35471079 ]
Williams E, Bachvaroff T, Place A: Dinoflagellate Phosphopantetheinyl Transferase (PPTase) and Thiolation Domain Interactions Characterized Using a Modified Indigoidine Synthesizing Reporter. Microorganisms. 2022 Mar 23;10(4):687. doi: 10.3390/microorganisms10040687. [PubMed:35456738 ]
LOTUS database [Link]

Showing NP-Card for (e)-5,5'-diamino-2,2'-dihydroxy-[3,3'-bipyridinylidene]-6,6'-dione (NP0211757)

MOL for NP0211757 ((e)-5,5'-diamino-2,2'-dihydroxy-[3,3'-bipyridinylidene]-6,6'-dione)

3D MOL for NP0211757 ((e)-5,5'-diamino-2,2'-dihydroxy-[3,3'-bipyridinylidene]-6,6'-dione)

3D SDF for NP0211757 ((e)-5,5'-diamino-2,2'-dihydroxy-[3,3'-bipyridinylidene]-6,6'-dione)

3D-SDF for NP0211757 ((e)-5,5'-diamino-2,2'-dihydroxy-[3,3'-bipyridinylidene]-6,6'-dione)

PDB for NP0211757 ((e)-5,5'-diamino-2,2'-dihydroxy-[3,3'-bipyridinylidene]-6,6'-dione)

3D PDB for NP0211757 ((e)-5,5'-diamino-2,2'-dihydroxy-[3,3'-bipyridinylidene]-6,6'-dione)

SMILES for NP0211757 ((e)-5,5'-diamino-2,2'-dihydroxy-[3,3'-bipyridinylidene]-6,6'-dione)

INCHI for NP0211757 ((e)-5,5'-diamino-2,2'-dihydroxy-[3,3'-bipyridinylidene]-6,6'-dione)

Structure for NP0211757 ((e)-5,5'-diamino-2,2'-dihydroxy-[3,3'-bipyridinylidene]-6,6'-dione)

3D Structure for NP0211757 ((e)-5,5'-diamino-2,2'-dihydroxy-[3,3'-bipyridinylidene]-6,6'-dione)