NP-MRD: Showing NP-Card for Cylindradine B (NP0081985)

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Record Information

Version

2.0

Created at

2022-04-29 03:02:31 UTC

Updated at

2022-04-29 03:02:31 UTC

NP-MRD ID

NP0081985

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cylindradine B

Description

(1R,5R,14S,15S)-8,9-dibromo-14,15-dihydroxy-3-imino-2,4,7,12-tetraazatetracyclo[10.3.0.0¹,⁵.0⁶,¹⁰]Pentadeca-6(10),8-dien-11-one belongs to the class of organic compounds known as aryl bromides. These are organic compounds containing the acyl bromide functional group. Cylindradine B is found in Axinella cylindratus. Based on a literature review very few articles have been published on (1R,5R,14S,15S)-8,9-dibromo-14,15-dihydroxy-3-imino-2,4,7,12-tetraazatetracyclo[10.3.0.0¹,⁵.0⁶,¹⁰]Pentadeca-6(10),8-dien-11-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 35  0  0  0  0  0  0  0  0999 V2000
    0.3330   -3.1034    2.0693 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2883   -2.0075    1.1624 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9667   -1.9585    0.0840 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7053   -0.7095   -0.6286 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8584    0.1777   -0.3506 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1934   -0.0151   -0.4308 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8493    1.0917   -0.0819 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7585    1.3471   -0.0251 Br  0  0  0  0  0  0  0  0  0  0  0  0
    2.9378    2.0601    0.2433 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2968    3.8485    0.8164 Br  0  0  0  0  0  0  0  0  0  0  0  0
    1.6819    1.4679    0.0690 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3564    2.0431    0.2807 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1965    3.2168    0.6615 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7448    1.1655    0.0204 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1397    1.4426   -0.2426 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6445    0.2753   -1.0424 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9337   -0.1108   -0.6096 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7016   -0.8606   -0.8049 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2545   -1.3758   -2.0055 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5651   -0.2459   -0.0063 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5020   -0.8335    1.3226 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4963   -3.7112    2.1612 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2260   -3.2433    2.6124 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5951   -0.9168   -1.7155 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6361   -0.9193   -0.7289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6681    1.4984    0.7386 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2869    2.4138   -0.7571 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6867    0.5875   -2.1084 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2832    0.5899   -0.0028 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1558   -1.6662   -0.1876 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8714   -1.0804   -2.7216 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9451   -0.4683    2.2084 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5 11  2  0
 11  9  1  0
  9 10  1  0
  9  7  2  0
  7  8  1  0
  7  6  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 18 20  1  0
 20 21  1  1
 21  2  1  0
 20  4  1  0
  6  5  1  0
 20 14  1  0
  1 22  1  0
  1 23  1  0
  4 24  1  6
  6 25  1  0
 15 26  1  0
 15 27  1  0
 16 28  1  6
 17 29  1  0
 18 30  1  1
 19 31  1  0
 21 32  1  0
M  END


  Mrv1652304292205022D          

 21 24  0  0  1  0            999 V2000
    3.3523    1.9354    0.0000 C   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    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -0.1271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4663    3.1549    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6458    3.2412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3102    2.4875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2333    3.9556    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712    1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    2.9750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1369    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6218    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1369    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.4468    1.5229    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    4.3918    0.0709    0.0000 Br  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
  3  5  1  0  0  0  0
  6  5  1  6  0  0  0
  6  7  1  0  0  0  0
  1  7  1  0  0  0  0
  7  8  1  6  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  6 10  1  0  0  0  0
  9 11  1  0  0  0  0
  6 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
  5 14  1  0  0  0  0
 13 15  1  6  0  0  0
 12 16  1  1  0  0  0
  2 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
  1 19  1  0  0  0  0
 18 20  1  0  0  0  0
 17 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0081985

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=N[C@@H]2C3=C(C(Br)=C(Br)N3)C(=O)N3C[C@H](O)[C@@H](O)[C@@]23N1

> <INCHI_IDENTIFIER>
InChI=1S/C11H11Br2N5O3/c12-4-3-5(15-8(4)13)6-11(17-10(14)16-6)7(20)2(19)1-18(11)9(3)21/h2,6-7,15,19-20H,1H2,(H3,14,16,17)/t2-,6+,7+,11+/m0/s1

> <INCHI_KEY>
PMIAEKSPKCHUBL-PJFHXCITSA-N

> <FORMULA>
C11H11Br2N5O3

> <MOLECULAR_WEIGHT>
421.049

> <EXACT_MASS>
418.922865

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
32.273223178785

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,5R,14S,15S)-3-amino-8,9-dibromo-14,15-dihydroxy-2,4,7,12-tetraazatetracyclo[10.3.0.0^{1,5}.0^{6,10}]pentadeca-3,6(10),8-trien-11-one

> <ALOGPS_LOGP>
-0.11

> <JCHEM_LOGP>
-0.6306346310000004

> <ALOGPS_LOGS>
-2.83

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.873774065973567

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.977099679317316

> <JCHEM_PKA_STRONGEST_BASIC>
8.349244626244674

> <JCHEM_POLAR_SURFACE_AREA>
126.97

> <JCHEM_REFRACTIVITY>
78.79690000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.20e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,5R,14S,15S)-3-amino-8,9-dibromo-14,15-dihydroxy-2,4,7,12-tetraazatetracyclo[10.3.0.0^{1,5}.0^{6,10}]pentadeca-3,6(10),8-trien-11-one

> <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       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.924  -0.237   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       3.590   2.073   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       4.604   5.889   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       3.072   6.050   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       2.446   4.643   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       2.302   7.384   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       2.126   4.089   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -0.320   2.843   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       1.650   5.553   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       7.722   1.597   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.627   2.843   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       7.722   4.089   0.000  0.00  0.00           N+0
HETATM   20 Br   UNK     0      10.167   2.843   0.000  0.00  0.00          Br+0
HETATM   21 Br   UNK     0       8.198   0.132   0.000  0.00  0.00          Br+0
CONECT    1    2    7   19                                                  
CONECT    2    1    3   17                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   14                                                  
CONECT    6    5    7   10   12                                             
CONECT    7    6    1    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9    6                                                       
CONECT   11    9                                                            
CONECT   12    6   13   16                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13    5                                                       
CONECT   15   13                                                            
CONECT   16   12                                                            
CONECT   17    2   18   21                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18    1                                                       
CONECT   20   18                                                            
CONECT   21   17                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   48    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₁₁Br₂N₅O₃

Average Mass

421.0490 Da

Monoisotopic Mass

418.92286 Da

IUPAC Name

(1R,5R,14S,15S)-3-amino-8,9-dibromo-14,15-dihydroxy-2,4,7,12-tetraazatetracyclo[10.3.0.0^{1,5}.0^{6,10}]pentadeca-3,6(10),8-trien-11-one

Traditional Name

(1R,5R,14S,15S)-3-amino-8,9-dibromo-14,15-dihydroxy-2,4,7,12-tetraazatetracyclo[10.3.0.0^{1,5}.0^{6,10}]pentadeca-3,6(10),8-trien-11-one

CAS Registry Number

Not Available

SMILES

NC1=N[C@@H]2C3=C(C(Br)=C(Br)N3)C(=O)N3C[C@H](O)[C@@H](O)[C@@]23N1

InChI Identifier

InChI=1S/C11H11Br2N5O3/c12-4-3-5(15-8(4)13)6-11(17-10(14)16-6)7(20)2(19)1-18(11)9(3)21/h2,6-7,15,19-20H,1H2,(H3,14,16,17)/t2-,6+,7+,11+/m0/s1

InChI Key

PMIAEKSPKCHUBL-PJFHXCITSA-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
Axinella cylindratus	Animalia	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aryl bromides. These are organic compounds containing the acyl bromide functional group.

Kingdom

Organic compounds

Super Class

Organohalogen compounds

Class

Aryl halides

Sub Class

Aryl bromides

Direct Parent

Aryl bromides

Alternative Parents

Substituents

Aryl bromide
Substituted pyrrole
2-imidazoline
Pyrrole
Pyrrolidine
Heteroaromatic compound
Tertiary carboxylic acid amide
Vinylogous amide
Vinylogous halide
1,2-diol
Carboxamide group
Guanidine
Lactam
Secondary alcohol
Carboxylic acid derivative
Azacycle
Organoheterocyclic compound
Carboximidamide
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organonitrogen compound
Organobromide
Organic oxygen compound
Amine
Alcohol
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
logP	-0.11	ALOGPS
logP	-0.63	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	10.98	ChemAxon
pKa (Strongest Basic)	8.35	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	126.97 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	78.8 m³·mol⁻¹	ChemAxon
Polarizability	32.27 Å³	ChemAxon
Number of Rings	4	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

27023829

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25170158

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Cylindradine B (NP0081985)

MOL for NP0081985 (Cylindradine B)

3D MOL for NP0081985 (Cylindradine B)

3D SDF for NP0081985 (Cylindradine B)

3D-SDF for NP0081985 (Cylindradine B)

PDB for NP0081985 (Cylindradine B)

3D PDB for NP0081985 (Cylindradine B)

SMILES for NP0081985 (Cylindradine B)

INCHI for NP0081985 (Cylindradine B)

Structure for NP0081985 (Cylindradine B)

3D Structure for NP0081985 (Cylindradine B)