NP-MRD: Showing NP-Card for Didemnimide D (NP0069815)

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Record Information

Version

2.0

Created at

2022-04-28 15:08:51 UTC

Updated at

2022-04-28 15:08:51 UTC

NP-MRD ID

NP0069815

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Didemnimide D

Description

Didemnimide D belongs to the class of organic compounds known as indoles. Indoles are compounds containing an indole moiety, which consists of pyrrole ring fused to benzene to form 2,3-benzopyrrole. Didemnimide D is found in Didemnum conchyliatum and Didemnum granulatum. Didemnimide D is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 37  0  0  0  0  0  0  0  0999 V2000
   -3.4465   -1.0556    0.4656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8747    0.1409    1.0659 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1505    0.5990    2.3126 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4487    1.7354    2.5099 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7513    1.9671    1.3949 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0074    0.9563    0.4531 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4019    0.8846   -0.8701 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2953    0.2111   -1.2040 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5195   -0.6029   -0.3171 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1895   -1.6416    0.5160 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3159   -2.0383    1.1940 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3627   -1.2882    0.8230 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6795   -1.2895    1.2186 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5523   -0.3869    0.6788 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4071   -0.3025    1.1768 Br  0  0  0  0  0  0  0  0  0  0  0  0
    4.1228    0.5347   -0.2695 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7951    0.4997   -0.6357 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8824   -0.3846   -0.1246 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0926    0.4471   -2.6459 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8555   -0.0327   -3.3082 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1200    1.2764   -3.1244 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9623    1.5698   -2.0282 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9955    2.2974   -2.0969 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5561   -1.0358    0.4816 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0564   -1.1644   -0.5772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1455   -1.9099    1.1176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8247    0.0851    2.9774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0908    2.7858    1.2031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7927   -2.0714    0.6119 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3019   -2.8163    1.8836 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0293   -1.9961    1.9453 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7833    1.2518   -0.7089 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3935    1.1961   -1.3827 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1776    1.5784   -4.1237 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8 19  1  0
 19 20  2  0
 19 21  1  0
 21 22  1  0
 22 23  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  1  0
 14 16  2  0
 16 17  1  0
 17 18  2  0
  6  2  1  0
 22  7  1  0
 18  9  1  0
 18 12  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  0
  5 28  1  0
 21 34  1  0
 10 29  1  0
 11 30  1  0
 13 31  1  0
 16 32  1  0
 17 33  1  0
M  END


  Mrv1533004191518152D          

 23 26  0  0  0  0            999 V2000
   -1.6078   -2.9596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3529   -2.1750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8378   -1.5075    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3529   -0.8401    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -1.0950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -1.9200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -2.4049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3687   -2.8174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1937   -2.8174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -3.4849    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -3.2299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -3.7149    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    0.1271    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
  7 12  1  0  0  0  0
 12 13  2  0  0  0  0
  8 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 14 23  1  0  0  0  0
 17 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0069815

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1C=NC=C1C1=C(C(=O)NC1=O)C1=CNC2=CC(Br)=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C16H11BrN4O2/c1-21-7-18-6-12(21)14-13(15(22)20-16(14)23)10-5-19-11-4-8(17)2-3-9(10)11/h2-7,19H,1H3,(H,20,22,23)

> <INCHI_KEY>
UGQSNWJOZBAEMD-UHFFFAOYSA-N

> <FORMULA>
C16H11BrN4O2

> <MOLECULAR_WEIGHT>
371.194

> <EXACT_MASS>
370.006539

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
33.274214922096725

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-(6-bromo-1H-indol-3-yl)-4-(1-methyl-1H-imidazol-5-yl)-2,5-dihydro-1H-pyrrole-2,5-dione

> <ALOGPS_LOGP>
2.26

> <JCHEM_LOGP>
1.5929944503333333

> <ALOGPS_LOGS>
-3.99

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.732659196602569

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.817695007509629

> <JCHEM_PKA_STRONGEST_BASIC>
5.7866421632290175

> <JCHEM_POLAR_SURFACE_AREA>
79.78

> <JCHEM_REFRACTIVITY>
88.6939

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.79e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-(6-bromo-1H-indol-3-yl)-4-(3-methylimidazol-4-yl)-1H-pyrrole-2,5-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-15         0                                  
HETATM    1  C   UNK     0      -3.001  -5.525   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -2.525  -4.060   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -3.431  -2.814   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      -2.525  -1.568   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -1.061  -2.044   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.061  -3.584   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.185  -4.489   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.555  -5.259   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       4.095  -5.259   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0       1.650  -6.505   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       0.185  -6.029   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -1.061  -6.934   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   20 Br   UNK     0       7.591   0.237   0.000  0.00  0.00          Br+0
HETATM   21  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    2    7                                                  
CONECT    7    6    8   12                                                  
CONECT    8    7    9   14                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11    7   13                                                  
CONECT   13   12                                                            
CONECT   14    8   15   23                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   23                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   14   17                                                  
MASTER        0    0    0    0    0    0    0    0   23    0   52    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₆H₁₁BrN₄O₂

Average Mass

371.1940 Da

Monoisotopic Mass

370.00654 Da

IUPAC Name

3-(6-bromo-1H-indol-3-yl)-4-(1-methyl-1H-imidazol-5-yl)-2,5-dihydro-1H-pyrrole-2,5-dione

Traditional Name

3-(6-bromo-1H-indol-3-yl)-4-(3-methylimidazol-4-yl)-1H-pyrrole-2,5-dione

CAS Registry Number

Not Available

SMILES

CN1C=NC=C1C1=C(C(=O)NC1=O)C1=CNC2=CC(Br)=CC=C12

InChI Identifier

InChI=1S/C16H11BrN4O2/c1-21-7-18-6-12(21)14-13(15(22)20-16(14)23)10-5-19-11-4-8(17)2-3-9(10)11/h2-7,19H,1H3,(H,20,22,23)

InChI Key

UGQSNWJOZBAEMD-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Didemnum conchyliatum	Animalia	KNApSAcK
Didemnum granulatum	Animalia	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as indoles. Indoles are compounds containing an indole moiety, which consists of pyrrole ring fused to benzene to form 2,3-benzopyrrole.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indoles

Direct Parent

Indoles

Alternative Parents

Substituents

Indole
Maleimide
Aryl bromide
Aryl halide
Benzenoid
Substituted pyrrole
N-substituted imidazole
Azole
Carboxylic acid imide
Dicarboximide
Heteroaromatic compound
Imidazole
Pyrroline
Pyrrole
Carboxylic acid imide, n-unsubstituted
Carboxylic acid derivative
Azacycle
Organonitrogen compound
Organooxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organopnictogen compound
Organic oxygen compound
Organobromide
Organohalogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

indoles (CHEBI:67329 )

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	2.26	ALOGPS
logP	1.59	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Acidic)	9.82	ChemAxon
pKa (Strongest Basic)	5.79	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	79.78 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	88.69 m³·mol⁻¹	ChemAxon
Polarizability	33.27 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10785428

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Didemnimide D (NP0069815)

MOL for NP0069815 (Didemnimide D)

3D MOL for NP0069815 (Didemnimide D)

3D SDF for NP0069815 (Didemnimide D)

3D-SDF for NP0069815 (Didemnimide D)

PDB for NP0069815 (Didemnimide D)

3D PDB for NP0069815 (Didemnimide D)

SMILES for NP0069815 (Didemnimide D)

INCHI for NP0069815 (Didemnimide D)

Structure for NP0069815 (Didemnimide D)

3D Structure for NP0069815 (Didemnimide D)