NP-MRD: Showing NP-Card for (1r,9r,10s,14s)-3,4-dibromo-12,14-dihydroxy-2,8,11,13-tetraazatetracyclo[7.6.0.0²,⁶.0¹⁰,¹⁴]pentadeca-3,5,11-trien-7-one (NP0253517)

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Record Information

Version

2.0

Created at

2022-09-07 17:24:28 UTC

Updated at

2022-09-07 17:24:28 UTC

NP-MRD ID

NP0253517

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,9r,10s,14s)-3,4-dibromo-12,14-dihydroxy-2,8,11,13-tetraazatetracyclo[7.6.0.0²,⁶.0¹⁰,¹⁴]pentadeca-3,5,11-trien-7-one

Description

Agelastatin F belongs to the class of organic compounds known as 2-heteroaryl carboxamides. 2-Heteroaryl carboxamides are compounds containing a heteroaromatic ring that carries a carboxamide group. (1r,9r,10s,14s)-3,4-dibromo-12,14-dihydroxy-2,8,11,13-tetraazatetracyclo[7.6.0.0²,⁶.0¹⁰,¹⁴]pentadeca-3,5,11-trien-7-one was first documented in 2010 (PMID: 20166736). Based on a literature review very few articles have been published on agelastatin F.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309072219242D          

 20 23  0  0  1  0            999 V2000
    2.3553    2.4712    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7422    1.7425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5667    1.7133    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9536    0.9847    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.7540    0.7847    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.5191    1.0934    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.0491    0.4611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8721    0.5182    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6115   -0.2383    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8112   -0.0383    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.8683   -0.8613    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0461   -0.3470    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5161    0.2853    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6916    0.3145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3047    1.0431    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4921    0.9003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3769    0.0833    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6483   -0.3036    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    2.1182   -0.2787    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2611   -1.0912    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
  4  3  1  1  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  5 10  1  0  0  0  0
 10 11  1  1  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
  4 13  1  0  0  0  0
 13 14  1  1  0  0  0
 14 15  1  0  0  0  0
  2 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
 14 19  1  0  0  0  0
 19 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0253517

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=N[C@H]2[C@@H]3NC(=O)C4=CC(Br)=C(Br)N4[C@@H]3C[C@@]2(O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C11H10Br2N4O3/c12-3-1-4-9(18)14-6-5(17(4)8(3)13)2-11(20)7(6)15-10(19)16-11/h1,5-7,20H,2H2,(H,14,18)(H2,15,16,19)/t5-,6-,7+,11+/m1/s1

> <INCHI_KEY>
XDTDQGZBMQLKIM-MNRJBDMISA-N

> <FORMULA>
C11H10Br2N4O3

> <MOLECULAR_WEIGHT>
406.034

> <EXACT_MASS>
403.911966

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
30.287089926380634

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,9S,10S,14S)-3,4-dibromo-12,14-dihydroxy-2,8,11,13-tetraazatetracyclo[7.6.0.0^{2,6}.0^{10,14}]pentadeca-3,5,11-trien-7-one

> <JCHEM_LOGP>
1.1567942043333332

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.820032208573156

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.469487551333325

> <JCHEM_PKA_STRONGEST_BASIC>
2.3350511275642534

> <JCHEM_POLAR_SURFACE_AREA>
98.88

> <JCHEM_REFRACTIVITY>
74.7753

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,9S,10S,14S)-3,4-dibromo-12,14-dihydroxy-2,8,11,13-tetraazatetracyclo[7.6.0.0^{2,6}.0^{10,14}]pentadeca-3,5,11-trien-7-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  O   UNK     0       4.396   4.613   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       5.119   3.253   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       6.658   3.198   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       7.380   1.838   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.874   1.465   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      10.302   2.041   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      11.292   0.861   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      12.828   0.967   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0      10.475  -0.445   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       8.981  -0.072   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       9.087  -1.608   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       7.553  -0.648   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.563   0.532   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       5.024   0.587   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       4.302   1.947   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.785   1.680   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.570   0.156   0.000  0.00  0.00           C+0
HETATM   18 Br   UNK     0       1.210  -0.567   0.000  0.00  0.00          Br+0
HETATM   19  C   UNK     0       3.954  -0.520   0.000  0.00  0.00           C+0
HETATM   20 Br   UNK     0       4.221  -2.037   0.000  0.00  0.00          Br+0
CONECT    1    2                                                            
CONECT    2    1    3   15                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   13                                                  
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9    5   11   12                                             
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12    4   14                                                  
CONECT   14   13   15   19                                                  
CONECT   15   14    2   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   14   20                                                  
CONECT   20   19                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   46    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₁₀Br₂N₄O₃

Average Mass

406.0340 Da

Monoisotopic Mass

403.91197 Da

IUPAC Name

(1R,9S,10S,14S)-3,4-dibromo-12,14-dihydroxy-2,8,11,13-tetraazatetracyclo[7.6.0.0^{2,6}.0^{10,14}]pentadeca-3,5,11-trien-7-one

Traditional Name

(1R,9S,10S,14S)-3,4-dibromo-12,14-dihydroxy-2,8,11,13-tetraazatetracyclo[7.6.0.0^{2,6}.0^{10,14}]pentadeca-3,5,11-trien-7-one

CAS Registry Number

Not Available

SMILES

OC1=N[C@H]2[C@@H]3NC(=O)C4=CC(Br)=C(Br)N4[C@@H]3C[C@@]2(O)N1

InChI Identifier

InChI=1S/C11H10Br2N4O3/c12-3-1-4-9(18)14-6-5(17(4)8(3)13)2-11(20)7(6)15-10(19)16-11/h1,5-7,20H,2H2,(H,14,18)(H2,15,16,19)/t5-,6-,7+,11+/m1/s1

InChI Key

XDTDQGZBMQLKIM-MNRJBDMISA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 2-heteroaryl carboxamides. 2-Heteroaryl carboxamides are compounds containing a heteroaromatic ring that carries a carboxamide group.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Carboxylic acid derivatives

Direct Parent

2-heteroaryl carboxamides

Alternative Parents

Substituents

2-heteroaryl carboxamide
Aryl bromide
Aryl halide
Imidazolidinone
Substituted pyrrole
Cyclic alcohol
Imidazolidine
Heteroaromatic compound
Pyrrole
Lactam
Carbonic acid derivative
Urea
Secondary carboxylic acid amide
Alkanolamine
Azacycle
Organoheterocyclic compound
Organohalogen compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Carbonyl group
Organic oxygen compound
Organobromide
Organonitrogen compound
Organooxygen 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
logP	1.16	ChemAxon
pKa (Strongest Acidic)	4.47	ChemAxon
pKa (Strongest Basic)	2.34	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	98.88 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	74.78 m³·mol⁻¹	ChemAxon
Polarizability	30.29 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

24679243

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

46209659

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Tilvi S, Moriou C, Martin MT, Gallard JF, Sorres J, Patel K, Petek S, Debitus C, Ermolenko L, Al-Mourabit A: Agelastatin E, agelastatin F, and benzosceptrin C from the marine sponge Agelas dendromorpha. J Nat Prod. 2010 Apr 23;73(4):720-3. doi: 10.1021/np900539j. [PubMed:20166736 ]
LOTUS database [Link]

Showing NP-Card for (1r,9r,10s,14s)-3,4-dibromo-12,14-dihydroxy-2,8,11,13-tetraazatetracyclo[7.6.0.0²,⁶.0¹⁰,¹⁴]pentadeca-3,5,11-trien-7-one (NP0253517)

MOL for NP0253517 ((1r,9r,10s,14s)-3,4-dibromo-12,14-dihydroxy-2,8,11,13-tetraazatetracyclo[7.6.0.0²,⁶.0¹⁰,¹⁴]pentadeca-3,5,11-trien-7-one)

3D MOL for NP0253517 ((1r,9r,10s,14s)-3,4-dibromo-12,14-dihydroxy-2,8,11,13-tetraazatetracyclo[7.6.0.0²,⁶.0¹⁰,¹⁴]pentadeca-3,5,11-trien-7-one)

3D SDF for NP0253517 ((1r,9r,10s,14s)-3,4-dibromo-12,14-dihydroxy-2,8,11,13-tetraazatetracyclo[7.6.0.0²,⁶.0¹⁰,¹⁴]pentadeca-3,5,11-trien-7-one)

3D-SDF for NP0253517 ((1r,9r,10s,14s)-3,4-dibromo-12,14-dihydroxy-2,8,11,13-tetraazatetracyclo[7.6.0.0²,⁶.0¹⁰,¹⁴]pentadeca-3,5,11-trien-7-one)

PDB for NP0253517 ((1r,9r,10s,14s)-3,4-dibromo-12,14-dihydroxy-2,8,11,13-tetraazatetracyclo[7.6.0.0²,⁶.0¹⁰,¹⁴]pentadeca-3,5,11-trien-7-one)

3D PDB for NP0253517 ((1r,9r,10s,14s)-3,4-dibromo-12,14-dihydroxy-2,8,11,13-tetraazatetracyclo[7.6.0.0²,⁶.0¹⁰,¹⁴]pentadeca-3,5,11-trien-7-one)

SMILES for NP0253517 ((1r,9r,10s,14s)-3,4-dibromo-12,14-dihydroxy-2,8,11,13-tetraazatetracyclo[7.6.0.0²,⁶.0¹⁰,¹⁴]pentadeca-3,5,11-trien-7-one)

INCHI for NP0253517 ((1r,9r,10s,14s)-3,4-dibromo-12,14-dihydroxy-2,8,11,13-tetraazatetracyclo[7.6.0.0²,⁶.0¹⁰,¹⁴]pentadeca-3,5,11-trien-7-one)

Structure for NP0253517 ((1r,9r,10s,14s)-3,4-dibromo-12,14-dihydroxy-2,8,11,13-tetraazatetracyclo[7.6.0.0²,⁶.0¹⁰,¹⁴]pentadeca-3,5,11-trien-7-one)

3D Structure for NP0253517 ((1r,9r,10s,14s)-3,4-dibromo-12,14-dihydroxy-2,8,11,13-tetraazatetracyclo[7.6.0.0²,⁶.0¹⁰,¹⁴]pentadeca-3,5,11-trien-7-one)