NP-MRD: Showing NP-Card for Dragmacidonamine A (NP0079013)

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Record Information

Version

2.0

Created at

2022-04-29 00:05:56 UTC

Updated at

2022-04-29 00:05:56 UTC

NP-MRD ID

NP0079013

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Dragmacidonamine A

Description

Dragmacidonamine A is found in Dragmacidon sp.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304292202052D          

 27 30  0  0  0  0            999 V2000
    2.6014   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3464    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8985    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7054    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9604    0.2410    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4084   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6633   -1.1567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4703   -1.3283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0834   -0.7762    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7978   -1.1887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6263   -1.9957    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8058   -2.0819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3933   -2.7964    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    4.8058   -3.5109    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1783   -2.6088    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9971    0.0442    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2575    1.6387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0645    1.4672    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0025    2.4233    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5214    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2665   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9339   -0.6855    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4595   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0925    0.2410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1624    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9694    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3896    1.6387    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  4  0  0  0  0
  9 10  4  0  0  0  0
 10 11  4  0  0  0  0
 11 12  4  0  0  0  0
  8 12  4  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 11 15  1  0  0  0  0
  9 16  1  0  0  0  0
  4 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
  2 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
  1 22  1  0  0  0  0
 21 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 20 26  1  0  0  0  0
 25 27  1  0  0  0  0
M  END


  Mrv1652304292202052D          

 27 30  0  0  0  0            999 V2000
    2.6014   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3464    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8985    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7054    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9604    0.2410    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4084   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6633   -1.1567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4703   -1.3283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0834   -0.7762    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7978   -1.1887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6263   -1.9957    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8058   -2.0819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3933   -2.7964    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    4.8058   -3.5109    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1783   -2.6088    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9971    0.0442    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2575    1.6387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0645    1.4672    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0025    2.4233    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5214    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2665   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9339   -0.6855    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4595   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0925    0.2410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1624    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9694    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3896    1.6387    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  4  0  0  0  0
  9 10  4  0  0  0  0
 10 11  4  0  0  0  0
 11 12  4  0  0  0  0
  8 12  4  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 11 15  1  0  0  0  0
  9 16  1  0  0  0  0
  4 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
  2 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
  1 22  1  0  0  0  0
 21 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 20 26  1  0  0  0  0
 25 27  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0079013

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CSc1c(CC2=NC(=CC3=C2NC2=C3C=C(O)C=C2)C(O)=O)n(C)cn1C

> <INCHI_IDENTIFIER>
InChI=1S/C19H19N4O3S/c1-22-9-23(2)18(27-3)16(22)8-14-17-12(7-15(20-14)19(25)26)11-6-10(24)4-5-13(11)21-17/h4-7,9,21,24H,8H2,1-3H3,(H,25,26)

> <INCHI_KEY>
KYBFPINWSSKRPP-UHFFFAOYSA-N

> <FORMULA>
C19H19N4O3S

> <MOLECULAR_WEIGHT>
383.45

> <EXACT_MASS>
383.117786662

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
46

> <JCHEM_AVERAGE_POLARIZABILITY>
40.34261345338579

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-{[1,3-dimethyl-5-(methylsulfanyl)imidazol-4-yl]methyl}-6-hydroxy-9H-pyrido[3,4-b]indole-3-carboxylic acid

> <ALOGPS_LOGP>
1.47

> <JCHEM_LOGP>
2.6240545285722665

> <ALOGPS_LOGS>
-3.39

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.439936749703968

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4493239034458334

> <JCHEM_PKA_STRONGEST_BASIC>
5.074080590459821

> <JCHEM_POLAR_SURFACE_AREA>
96.07000000000001

> <JCHEM_REFRACTIVITY>
104.1782

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.56e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-{[1,3-dimethyl-5-(methylsulfanyl)imidazol-4-yl]methyl}-6-hydroxy-9H-pyrido[3,4-b]indole-3-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       4.856  -0.374   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.380   1.090   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.410   2.235   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.917   1.914   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       7.393   0.450   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       6.362  -0.695   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.838  -2.159   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.344  -2.479   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       9.489  -1.449   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      10.823  -2.219   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      10.502  -3.725   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       8.971  -3.886   0.000  0.00  0.00           C+0
HETATM   13  S   UNK     0       8.201  -5.220   0.000  0.00  0.00           S+0
HETATM   14  C   UNK     0       8.971  -6.554   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      11.533  -4.870   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.328   0.083   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.947   3.059   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       9.454   2.739   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       7.471   4.524   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       2.840   1.090   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.364  -0.374   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0       3.610  -1.280   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0       0.858  -0.695   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -0.173   0.450   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.303   1.914   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.810   2.235   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -0.727   3.059   0.000  0.00  0.00           O+0
CONECT    1    2    6   22                                                  
CONECT    2    1    3   20                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   17                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   12                                                  
CONECT    9    8   10   16                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   15                                                  
CONECT   12   11    8   13                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15   11                                                            
CONECT   16    9                                                            
CONECT   17    4   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20    2   21   26                                                  
CONECT   21   20   22   23                                                  
CONECT   22   21    1                                                       
CONECT   23   21   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25   20                                                       
CONECT   27   25                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   60    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₉H₁₉N₄O₃S

Average Mass

383.4500 Da

Monoisotopic Mass

383.11779 Da

IUPAC Name

1-{[1,3-dimethyl-5-(methylsulfanyl)imidazol-4-yl]methyl}-6-hydroxy-9H-pyrido[3,4-b]indole-3-carboxylic acid

Traditional Name

1-{[1,3-dimethyl-5-(methylsulfanyl)imidazol-4-yl]methyl}-6-hydroxy-9H-pyrido[3,4-b]indole-3-carboxylic acid

CAS Registry Number

Not Available

SMILES

CSc1c(CC2=NC(=CC3=C2NC2=C3C=C(O)C=C2)C(O)=O)n(C)cn1C

InChI Identifier

InChI=1S/C19H19N4O3S/c1-22-9-23(2)18(27-3)16(22)8-14-17-12(7-15(20-14)19(25)26)11-6-10(24)4-5-13(11)21-17/h4-7,9,21,24H,8H2,1-3H3,(H,25,26)

InChI Key

KYBFPINWSSKRPP-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Dragmacidon sp.	Animalia	KNApSAcK

Chemical Taxonomy

Classification

Not classified

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	1.47	ALOGPS
logP	2.62	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Acidic)	1.45	ChemAxon
pKa (Strongest Basic)	5.07	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	96.07 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	104.18 m³·mol⁻¹	ChemAxon
Polarizability	40.34 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

Not Available

References

General References

Not Available

Showing NP-Card for Dragmacidonamine A (NP0079013)

MOL for NP0079013 (Dragmacidonamine A)

3D MOL for NP0079013 (Dragmacidonamine A)

3D SDF for NP0079013 (Dragmacidonamine A)

3D-SDF for NP0079013 (Dragmacidonamine A)

PDB for NP0079013 (Dragmacidonamine A)

3D PDB for NP0079013 (Dragmacidonamine A)

SMILES for NP0079013 (Dragmacidonamine A)

INCHI for NP0079013 (Dragmacidonamine A)

Structure for NP0079013 (Dragmacidonamine A)

3D Structure for NP0079013 (Dragmacidonamine A)