NP-MRD: Showing NP-Card for crystamidine (NP0199402)

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Record Information

Version

2.0

Created at

2022-09-04 18:02:24 UTC

Updated at

2022-09-04 18:02:24 UTC

NP-MRD ID

NP0199402

Secondary Accession Numbers

None

Natural Product Identification

Common Name

crystamidine

Description

Crystamidine belongs to the class of organic compounds known as erythrinanes. These are erythrina alkaloids possessing either a 6-5-6-6-membered indoloisoquinoline core or a derivative thereof. crystamidine is found in Erythrina americana, Erythrina brucei and Erythrina crista-galli. crystamidine was first documented in 2016 (PMID: 27145193). Based on a literature review very few articles have been published on Crystamidine (PMID: 34396757).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 38 42  0  0  0  0  0  0  0  0999 V2000
   -3.9115    1.3898   -1.2838 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5117    0.3070   -0.5249 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1807    0.4736   -0.1482 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1794    0.6130    1.3011 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5920   -0.3308    2.0715 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9721   -1.4723    1.3865 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9975   -2.7571    1.6661 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3187   -3.5025    0.5865 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1401   -4.7314    0.4795 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1032   -2.4710   -0.3414 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8972   -2.6133   -1.5226 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7329   -1.6284   -1.8430 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7647   -0.4526   -0.9788 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8077    0.4598   -1.1386 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0313    1.4628   -0.2261 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2050    1.5684    0.8722 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1546    0.6562    1.0328 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9160   -0.3396    0.1374 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2973   -1.1892    0.1345 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3652   -0.6020   -0.7705 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6548    2.6501    1.6194 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6270    3.3762    0.9066 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9781    2.4828   -0.1466 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9642    1.2961   -1.6034 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7528    2.3576   -0.7573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2197    1.4310   -2.1701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8563    1.4578   -0.5942 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6218    1.4342    1.8195 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5778   -0.2736    3.1291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4278   -3.2569    2.5331 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8329   -3.4871   -2.1461 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3748   -1.6945   -2.7223 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4399    0.3526   -2.0093 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5682    0.8071    1.9219 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8539   -0.2232   -1.6717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0199   -1.4343   -1.0867 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5075    3.5829    1.5599 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1648    4.3007    0.5278 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3 20  1  0
 19 20  1  6
 19 10  1  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 21  1  0
 21 22  1  0
 22 23  1  0
 16 17  1  0
 17 18  2  0
 10  8  1  0
  8  9  2  0
  8  7  1  0
  7  6  2  0
  6  5  1  0
  5  4  2  0
  4  3  1  0
 18 19  1  0
  6 19  1  0
 18 13  1  0
 23 15  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  6
 20 35  1  0
 20 36  1  0
 11 31  1  0
 12 32  1  0
 14 33  1  0
 22 37  1  0
 22 38  1  0
 17 34  1  0
  7 30  1  0
  5 29  1  0
  4 28  1  0
M  END


  Mrv1652309042220022D          

 23 27  0  0  1  0            999 V2000
    3.7329   -0.9612    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3245   -0.2444    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4995   -0.2397    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0829   -0.9518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2579   -0.9471    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8495   -0.2302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0436   -0.0541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0380    0.7669    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7501    1.1834    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7176    1.0981    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9770    1.8813    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7849    2.0482    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3335    1.4319    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1414    1.5988    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6899    0.9826    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4305    0.1995    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6226    0.0325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8935    0.7967    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2661    0.4819    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0911    0.4772    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0952   -0.2893    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7654    0.1918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5149    0.9779    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  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
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 13 18  1  0  0  0  0
 18 19  1  0  0  0  0
  6 19  1  0  0  0  0
 19 10  1  1  0  0  0
 19 20  1  0  0  0  0
  3 20  1  0  0  0  0
 16 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 15 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0199402

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO[C@@H]1C[C@@]23N(C=CC4=CC5=C(OCO5)C=C24)C(=O)C=C3C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C18H15NO4/c1-21-13-3-2-12-7-17(20)19-5-4-11-6-15-16(23-10-22-15)8-14(11)18(12,19)9-13/h2-8,13H,9-10H2,1H3/t13-,18-/m0/s1

> <INCHI_KEY>
NZMLLYZLUYBOGO-UGSOOPFHSA-N

> <FORMULA>
C18H15NO4

> <MOLECULAR_WEIGHT>
309.321

> <EXACT_MASS>
309.100107967

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
31.51733154493219

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,19R)-19-methoxy-5,7-dioxa-13-azapentacyclo[11.7.0.0^{1,16}.0^{2,10}.0^{4,8}]icosa-2,4(8),9,11,15,17-hexaen-14-one

> <JCHEM_LOGP>
1.344741794666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-2.210262294946236

> <JCHEM_POLAR_SURFACE_AREA>
48.0

> <JCHEM_REFRACTIVITY>
85.129

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,19R)-19-methoxy-5,7-dioxa-13-azapentacyclo[11.7.0.0^{1,16}.0^{2,10}.0^{4,8}]icosa-2,4(8),9,11,15,17-hexaen-14-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0       6.968  -1.794   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       6.206  -0.456   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       4.666  -0.447   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.888  -1.777   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.348  -1.768   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.586  -0.430   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.081  -0.101   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.071   1.431   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.400   2.209   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0       1.339   2.050   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       1.824   3.512   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.332   3.823   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.356   2.673   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.864   2.985   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.888   1.834   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.404   0.372   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.895   0.061   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.535   1.487   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.363   0.899   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.903   0.891   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       7.644  -0.540   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       8.895   0.358   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       8.428   1.825   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   20                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   19                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   19                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   18                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   23                                                  
CONECT   16   15   17   21                                                  
CONECT   17   16   18                                                       
CONECT   18   17   13   19                                                  
CONECT   19   18    6   10   20                                             
CONECT   20   19    3                                                       
CONECT   21   16   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   15                                                       
MASTER        0    0    0    0    0    0    0    0   23    0   54    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₈H₁₅NO₄

Average Mass

309.3210 Da

Monoisotopic Mass

309.10011 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CO[C@@H]1C[C@@]23N(C=CC4=CC5=C(OCO5)C=C24)C(=O)C=C3C=C1

InChI Identifier

InChI=1S/C18H15NO4/c1-21-13-3-2-12-7-17(20)19-5-4-11-6-15-16(23-10-22-15)8-14(11)18(12,19)9-13/h2-8,13H,9-10H2,1H3/t13-,18-/m0/s1

InChI Key

NZMLLYZLUYBOGO-UGSOOPFHSA-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
Erythrina americana	LOTUS Database	35616633
Erythrina brucei	LOTUS Database	35616633
Erythrina crista-galli	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as erythrinanes. These are erythrina alkaloids possessing either a 6-5-6-6-membered indoloisoquinoline core or a derivative thereof.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Erythrina alkaloids

Sub Class

Erythrinanes

Direct Parent

Erythrinanes

Alternative Parents

Substituents

Erythrinane skeleton
Benzodioxole
Indole or derivatives
Benzenoid
Pyrroline
Tertiary carboxylic acid amide
Carboxamide group
Lactam
Acetal
Carboxylic acid derivative
Dialkyl ether
Ether
Oxacycle
Azacycle
Organoheterocyclic compound
Carbonyl group
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Organic oxygen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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

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

52085384

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101922024

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Cai YS, Li Y, Chen ZC, Yu SS: [Erythrina alkaloids from stems of Erythrina corallodendron]. Zhongguo Zhong Yao Za Zhi. 2021 Jul;46(13):3368-3376. doi: 10.19540/j.cnki.cjcmm.20210331.201. [PubMed:34396757 ]
Umihara H, Yoshino T, Shimokawa J, Kitamura M, Fukuyama T: Development of a Divergent Synthetic Route to the Erythrina Alkaloids: Asymmetric Syntheses of 8-Oxo-erythrinine, Crystamidine, 8-Oxo-erythraline, and Erythraline. Angew Chem Int Ed Engl. 2016 Jun 6;55(24):6915-8. doi: 10.1002/anie.201602650. Epub 2016 May 4. [PubMed:27145193 ]
LOTUS database [Link]

Showing NP-Card for crystamidine (NP0199402)

MOL for NP0199402 (crystamidine)

3D MOL for NP0199402 (crystamidine)

3D SDF for NP0199402 (crystamidine)

3D-SDF for NP0199402 (crystamidine)

PDB for NP0199402 (crystamidine)

3D PDB for NP0199402 (crystamidine)

SMILES for NP0199402 (crystamidine)

INCHI for NP0199402 (crystamidine)

Structure for NP0199402 (crystamidine)

3D Structure for NP0199402 (crystamidine)