NP-MRD: Showing NP-Card for analogue (3) (NP0350948)

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Record Information

Version

2.0

Created at

2025-04-15 04:50:00 UTC

Updated at

2025-06-11 05:36:57 UTC

NP-MRD ID

NP0350948

Natural Product DOI

https://doi.org/10.57994/3933

Secondary Accession Numbers

None

Natural Product Identification

Common Name

analogue (3)

Description

analogue (3) was first documented in 2024 (PMID: 38964520). Based on a literature review a small amount of articles have been published on analogue (3) (PMID: 40123068) (PMID: 39818786).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 01262307162D          

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M  END


  Mrv2104 01262307162D          

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M  END
> <DATABASE_ID>
NP0350948

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)C[C@@H]1NC(=O)[C@H](CC2=CC=CC=C2)NC(=O)[C@H](CC2=CC=CC=C2)NC(=O)[C@H](CC2=CC=CC=C2)NC(=O)[C@H](CC2=CC=CC=C2)NC(=O)[C@H](CC2=CNC3=C2C=CC=C3)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C53H57N7O6/c1-34(2)27-42-48(61)60-47(32-39-33-54-41-26-16-15-25-40(39)41)53(66)59-46(31-38-23-13-6-14-24-38)52(65)58-45(30-37-21-11-5-12-22-37)51(64)57-44(29-36-19-9-4-10-20-36)50(63)56-43(49(62)55-42)28-35-17-7-3-8-18-35/h3-26,33-34,42-47,54H,27-32H2,1-2H3,(H,55,62)(H,56,63)(H,57,64)(H,58,65)(H,59,66)(H,60,61)/t42-,43-,44-,45-,46-,47-/m0/s1

> <INCHI_KEY>
CFDXPFASROSXIY-FQEQRRFLSA-N

> <FORMULA>
C53H57N7O6

> <MOLECULAR_WEIGHT>
888.082

> <EXACT_MASS>
887.437032583

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
123

> <JCHEM_AVERAGE_POLARIZABILITY>
93.34630114899039

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,6S,9S,12S,15S,18S)-3,6,9,12-tetrabenzyl-15-[(1H-indol-3-yl)methyl]-18-(2-methylpropyl)-1,4,7,10,13,16-hexaazacyclooctadecane-2,5,8,11,14,17-hexone

> <JCHEM_LOGP>
6.415390003666666

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.868651127236049

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.445647273321818

> <JCHEM_PKA_STRONGEST_BASIC>
-3.582248055557464

> <JCHEM_POLAR_SURFACE_AREA>
190.38999999999996

> <JCHEM_REFRACTIVITY>
251.63950000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6S,9S,12S,15S,18S)-3,6,9,12-tetrabenzyl-15-(1H-indol-3-ylmethyl)-18-(2-methylpropyl)-1,4,7,10,13,16-hexaazacyclooctadecane-2,5,8,11,14,17-hexone

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-JAN-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-JAN-23         0                                  
HETATM    1  O   UNK     0      -2.375  -1.770   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -3.406  -2.915   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.912  -2.595   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.388  -1.130   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.357   0.015   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.833   1.479   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.803   2.624   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.296   2.303   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.821   0.839   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.851  -0.306   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      -5.942  -3.739   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      -7.449  -3.419   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -8.479  -4.563   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -9.986  -4.243   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0     -10.461  -2.778   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0     -11.968  -2.458   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0     -12.444  -0.994   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0     -11.413   0.151   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -9.907  -0.169   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -9.431  -1.634   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0      -8.003  -6.028   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0      -9.034  -7.172   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -8.558  -8.637   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -9.588  -9.781   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0     -11.095  -9.461   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0     -12.125 -10.606   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0     -13.632 -10.285   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0     -14.107  -8.821   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0     -13.077  -7.676   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0     -11.571  -7.997   0.000  0.00  0.00           C+0
HETATM   31  N   UNK     0      -7.052  -8.957   0.000  0.00  0.00           N+0
HETATM   32  C   UNK     0      -6.576 -10.422   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -5.069 -10.742   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -4.593 -12.207   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -5.624 -13.351   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -5.148 -14.816   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -6.178 -15.960   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -7.685 -15.640   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -8.161 -14.175   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -7.130 -13.031   0.000  0.00  0.00           C+0
HETATM   41  N   UNK     0      -4.039  -9.597   0.000  0.00  0.00           N+0
HETATM   42  C   UNK     0      -2.533  -9.918   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      -1.502  -8.773   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       0.004  -9.093   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       0.480 -10.558   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      -0.425 -11.804   0.000  0.00  0.00           C+0
HETATM   47  N   UNK     0       0.480 -13.050   0.000  0.00  0.00           N+0
HETATM   48  C   UNK     0       1.945 -12.574   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0       1.945 -11.034   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0       3.278 -10.264   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0       4.612 -11.034   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0       4.612 -12.574   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0       3.278 -13.344   0.000  0.00  0.00           C+0
HETATM   54  N   UNK     0      -1.978  -7.309   0.000  0.00  0.00           N+0
HETATM   55  C   UNK     0      -0.947  -6.164   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      -1.423  -4.700   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      -0.393  -3.555   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0       1.113  -3.875   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0       2.144  -2.731   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0       1.589  -5.340   0.000  0.00  0.00           C+0
HETATM   61  N   UNK     0      -2.930  -4.379   0.000  0.00  0.00           N+0
HETATM   62  O   UNK     0       0.559  -6.484   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0      -2.057 -11.382   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0      -7.606 -11.566   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0     -10.540  -6.852   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0      -7.925  -1.954   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   61                                                  
CONECT    3    2    4   11                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    5                                                       
CONECT   11    3   12                                                       
CONECT   12   11   13   66                                                  
CONECT   13   12   14   21                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   15                                                       
CONECT   21   13   22                                                       
CONECT   22   21   23   65                                                  
CONECT   23   22   24   31                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   30                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   25                                                       
CONECT   31   23   32                                                       
CONECT   32   31   33   64                                                  
CONECT   33   32   34   41                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36   40                                                  
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   35                                                       
CONECT   41   33   42                                                       
CONECT   42   41   43   63                                                  
CONECT   43   42   44   54                                                  
CONECT   44   43   45                                                       
CONECT   45   44   46   49                                                  
CONECT   46   45   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47   49   53                                                  
CONECT   49   48   45   50                                                  
CONECT   50   49   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   53                                                       
CONECT   53   52   48                                                       
CONECT   54   43   55                                                       
CONECT   55   54   56   62                                                  
CONECT   56   55   57   61                                                  
CONECT   57   56   58                                                       
CONECT   58   57   59   60                                                  
CONECT   59   58                                                            
CONECT   60   58                                                            
CONECT   61   56    2                                                       
CONECT   62   55                                                            
CONECT   63   42                                                            
CONECT   64   32                                                            
CONECT   65   22                                                            
CONECT   66   12                                                            
MASTER        0    0    0    0    0    0    0    0   66    0  144    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₅₃H₅₇N₇O₆

Average Mass

888.0820 Da

Monoisotopic Mass

887.43703 Da

IUPAC Name

(3S,6S,9S,12S,15S,18S)-3,6,9,12-tetrabenzyl-15-[(1H-indol-3-yl)methyl]-18-(2-methylpropyl)-1,4,7,10,13,16-hexaazacyclooctadecane-2,5,8,11,14,17-hexone

Traditional Name

(3S,6S,9S,12S,15S,18S)-3,6,9,12-tetrabenzyl-15-(1H-indol-3-ylmethyl)-18-(2-methylpropyl)-1,4,7,10,13,16-hexaazacyclooctadecane-2,5,8,11,14,17-hexone

CAS Registry Number

Not Available

SMILES

CC(C)C[C@@H]1NC(=O)[C@H](CC2=CC=CC=C2)NC(=O)[C@H](CC2=CC=CC=C2)NC(=O)[C@H](CC2=CC=CC=C2)NC(=O)[C@H](CC2=CC=CC=C2)NC(=O)[C@H](CC2=CNC3=C2C=CC=C3)NC1=O

InChI Identifier

InChI=1S/C53H57N7O6/c1-34(2)27-42-48(61)60-47(32-39-33-54-41-26-16-15-25-40(39)41)53(66)59-46(31-38-23-13-6-14-24-38)52(65)58-45(30-37-21-11-5-12-22-37)51(64)57-44(29-36-19-9-4-10-20-36)50(63)56-43(49(62)55-42)28-35-17-7-3-8-18-35/h3-26,33-34,42-47,54H,27-32H2,1-2H3,(H,55,62)(H,56,63)(H,57,64)(H,58,65)(H,59,66)(H,60,61)/t42-,43-,44-,45-,46-,47-/m0/s1

InChI Key

CFDXPFASROSXIY-FQEQRRFLSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 400 MHz, C2D6OS, experimental)	seetharamsing.b@ntu.edu.sg	Nanyang Technological University	Balamkundu Seetharamsing	2025-04-15	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

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	6.42	ChemAxon
pKa (Strongest Acidic)	10.45	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	190.39 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	251.64 m³·mol⁻¹	ChemAxon
Polarizability	93.35 Å³	ChemAxon
Number of Rings	7	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

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Fan J, Zhang M, Qi B, Qiu H, Mi X, Zhou G, Zhang L, Liu X, Wang J, Wang X, Tu PF, Shi SP: Characterization and Synthesis of Alkaloidal Butenolides with Seed Germination Stimulating Properties from Angelica dahurica. J Agric Food Chem. 2025 Apr 2;73(13):7822-7832. doi: 10.1021/acs.jafc.5c00528. Epub 2025 Mar 23. [PubMed:40123068 ]
Scalvini L, Pala D, Cuzzolin A, Galvani F, Lodola A, Rivara S, Mor M, Rizzi A: JAK3 Inhibitors: Covalent and Noncovalent Interactions of a Cyanamide Group Investigated by Multiscale Free-Energy Simulations. J Chem Inf Model. 2025 Feb 10;65(3):1404-1418. doi: 10.1021/acs.jcim.4c01889. Epub 2025 Jan 16. [PubMed:39818786 ]
Al Subeh ZY, Pierre HC, Bockbrader RH, Tokarski RJ 2nd, Maldonado AC, Haughan MA, Rangel-Grimaldo ME, Pearce CJ, Burdette JE, Fuchs JR, Oberlies NH: Semisynthetic derivatives of the fungal metabolite eupenifeldin via targeting the tropolone hydroxy groups. Bioorg Med Chem Lett. 2024 Sep 15;110:129875. doi: 10.1016/j.bmcl.2024.129875. Epub 2024 Jul 2. [PubMed:38964520 ]

Showing NP-Card for analogue (3) (NP0350948)

MOL for NP0350948 (analogue (3))

3D MOL for NP0350948 (analogue (3))

3D SDF for NP0350948 (analogue (3))

3D-SDF for NP0350948 (analogue (3))

PDB for NP0350948 (analogue (3))

3D PDB for NP0350948 (analogue (3))

SMILES for NP0350948 (analogue (3))

INCHI for NP0350948 (analogue (3))

Structure for NP0350948 (analogue (3))

3D Structure for NP0350948 (analogue (3))