NP-MRD: Showing NP-Card for Brasilicardin D (NP0044050)

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Record Information

Version

1.0

Created at

2021-11-12 23:47:19 UTC

Updated at

2021-11-26 17:44:51 UTC

NP-MRD ID

NP0044050

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Brasilicardin D

Description

It was first documented in 2004 (PMID: 15465331).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652311132100472D          

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M  END


  Mrv1652311132100472D          

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    1.1270    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9520   -0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6020   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4587   -1.1144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3772   -0.5841    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0145    0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.8395    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0145    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8395    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.2520    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0770    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.4895    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4895    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.3145    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0770    2.5559    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.4895    3.2704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2520    2.5559    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.8395    3.2704    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  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  6  0  0  0
 10 12  1  0  0  0  0
 12 13  1  1  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
 12 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
  4 24  1  0  0  0  0
 10 24  1  0  0  0  0
 24 25  1  1  0  0  0
  6 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 26 29  1  0  0  0  0
  2 29  1  0  0  0  0
 29 30  1  1  0  0  0
  2 31  1  6  0  0  0
 32 31  1  1  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  6  0  0  0
 34 36  1  0  0  0  0
 36 37  1  1  0  0  0
 36 38  1  0  0  0  0
 38 39  1  6  0  0  0
 38 40  1  0  0  0  0
 32 40  1  0  0  0  0
 40 41  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0044050

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]1(C[C@]2(C)[C@]([H])(CC[C@@]3(C)[C@@H](CC[C@H](N)C(O)=O)C(C)=CC[C@]23[H])C(C)(C)[C@@H]1O)O[C@@H]1O[C@@H](C)[C@H](O)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C29H49NO8/c1-14-7-10-20-28(5,16(14)8-9-17(30)25(35)36)12-11-19-27(3,4)24(34)18(13-29(19,20)6)38-26-23(33)22(32)21(31)15(2)37-26/h7,15-24,26,31-34H,8-13,30H2,1-6H3,(H,35,36)/t15-,16-,17-,18-,19+,20-,21-,22+,23+,24+,26-,28-,29+/m0/s1

> <INCHI_KEY>
YJCRQRQABJDMCD-FGGMZTLESA-N

> <FORMULA>
C29H49NO8

> <MOLECULAR_WEIGHT>
539.71

> <EXACT_MASS>
539.345817542

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
87

> <JCHEM_AVERAGE_POLARIZABILITY>
60.32346505041185

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-4-[(1S,4aS,4bS,6S,7S,8aS,10aS)-7-hydroxy-2,4b,8,8,10a-pentamethyl-6-{[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}-1,4,4a,4b,5,6,7,8,8a,9,10,10a-dodecahydrophenanthren-1-yl]-2-aminobutanoic acid

> <ALOGPS_LOGP>
-0.48

> <JCHEM_LOGP>
-0.23420044468306742

> <ALOGPS_LOGS>
-3.64

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.212473427827232

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.579102580816689

> <JCHEM_PKA_STRONGEST_BASIC>
9.525011993318293

> <JCHEM_POLAR_SURFACE_AREA>
162.7

> <JCHEM_REFRACTIVITY>
140.8858

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.23e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-4-[(1S,4aS,4bS,6S,7S,8aS,10aS)-7-hydroxy-2,4b,8,8,10a-pentamethyl-6-{[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}-4,4a,5,6,7,8a,9,10-octahydro-1H-phenanthren-1-yl]-2-aminobutanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 13-NOV-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-NOV-21         0                                  
HETATM    1  H   UNK     0       8.264   2.104   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       6.724   2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.184   2.104   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.414   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.184  -0.564   0.000  0.00  0.00           C+0
HETATM    7  H   UNK     0       5.954  -1.897   0.000  0.00  0.00           H+0
HETATM    8  C   UNK     0       4.414  -1.897   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.874  -1.897   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.104  -0.564   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334  -1.897   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.564  -0.564   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.206  -1.897   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.746  -1.897   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.516  -3.231   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0      -1.746  -4.565   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0      -4.056  -3.231   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -4.826  -4.565   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -4.826  -1.897   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -0.206   0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.746   0.770   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.564   2.104   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.104   2.104   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM   25  H   UNK     0       3.644  -0.564   0.000  0.00  0.00           H+0
HETATM   26  C   UNK     0       6.724  -0.564   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.456  -2.080   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       8.171  -1.090   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       7.494   0.770   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       9.034   0.770   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       7.494   3.437   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       9.034   3.437   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       9.804   2.104   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      11.344   2.104   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      12.114   0.770   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      12.114   3.437   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      13.654   3.437   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      11.344   4.771   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      12.114   6.105   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0       9.804   4.771   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0       9.034   6.105   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   29   31                                             
CONECT    3    2    4                                                       
CONECT    4    3    5    6   24                                             
CONECT    5    4                                                            
CONECT    6    4    7    8   26                                             
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12   24                                             
CONECT   11   10                                                            
CONECT   12   10   13   20                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   12   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23    4   10   25                                             
CONECT   25   24                                                            
CONECT   26    6   27   28   29                                             
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29   26    2   30                                                  
CONECT   30   29                                                            
CONECT   31    2   32                                                       
CONECT   32   31   33   40                                                  
CONECT   33   32   34                                                       
CONECT   34   33   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   39   40                                                  
CONECT   39   38                                                            
CONECT   40   38   32   41                                                  
CONECT   41   40                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   88    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₄₉NO₈

Average Mass

539.7100 Da

Monoisotopic Mass

539.34582 Da

IUPAC Name

(2S)-4-[(1S,4aS,4bS,6S,7S,8aS,10aS)-7-hydroxy-2,4b,8,8,10a-pentamethyl-6-{[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}-1,4,4a,4b,5,6,7,8,8a,9,10,10a-dodecahydrophenanthren-1-yl]-2-aminobutanoic acid

Traditional Name

(2S)-4-[(1S,4aS,4bS,6S,7S,8aS,10aS)-7-hydroxy-2,4b,8,8,10a-pentamethyl-6-{[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}-4,4a,5,6,7,8a,9,10-octahydro-1H-phenanthren-1-yl]-2-aminobutanoic acid

CAS Registry Number

Not Available

SMILES

[H][C@@]1(C[C@]2(C)[C@]([H])(CC[C@@]3(C)[C@@H](CC[C@H](N)C(O)=O)C(C)=CC[C@]23[H])C(C)(C)[C@@H]1O)O[C@@H]1O[C@@H](C)[C@H](O)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C29H49NO8/c1-14-7-10-20-28(5,16(14)8-9-17(30)25(35)36)12-11-19-27(3,4)24(34)18(13-29(19,20)6)38-26-23(33)22(32)21(31)15(2)37-26/h7,15-24,26,31-34H,8-13,30H2,1-6H3,(H,35,36)/t15-,16-,17-,18-,19+,20-,21-,22+,23+,24+,26-,28-,29+/m0/s1

InChI Key

YJCRQRQABJDMCD-FGGMZTLESA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 150 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 250 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 175 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 225 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 125 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Nocardia brasiliensis IFM0406

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	-0.48	ALOGPS
logP	-0.23	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	2.58	ChemAxon
pKa (Strongest Basic)	9.53	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	162.7 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	140.89 m³·mol⁻¹	ChemAxon
Polarizability	60.32 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

Not Available

References

General References

Komatsu K, Tsuda M, Shiro M, Tanaka Y, Mikami Y, Kobayashi J: Brasilicardins B-D, new tricyclic terpenoids [correction of terpernoids] from actinomycete Nocardia brasiliensis. Bioorg Med Chem. 2004 Nov 1;12(21):5545-51. doi: 10.1016/j.bmc.2004.08.007. [PubMed:15465331 ]

Showing NP-Card for Brasilicardin D (NP0044050)

MOL for NP0044050 (Brasilicardin D)

3D MOL for NP0044050 (Brasilicardin D)

3D SDF for NP0044050 (Brasilicardin D)

3D-SDF for NP0044050 (Brasilicardin D)

PDB for NP0044050 (Brasilicardin D)

3D PDB for NP0044050 (Brasilicardin D)

SMILES for NP0044050 (Brasilicardin D)

INCHI for NP0044050 (Brasilicardin D)

Structure for NP0044050 (Brasilicardin D)

3D Structure for NP0044050 (Brasilicardin D)