NP-MRD: Showing NP-Card for Comp3 (NP0350921)

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Record Information

Version

2.0

Created at

2025-04-08 15:51:01 UTC

Updated at

2025-07-24 18:35:52 UTC

NP-MRD ID

NP0350921

Natural Product DOI

https://doi.org/10.57994/3906

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Comp3

Description

Comp3 was first documented in 2021 (PMID: 33495861). Based on a literature review a small amount of articles have been published on Comp3 (PMID: 37702159) (PMID: 36816262) (PMID: 37513188) (PMID: 38822803).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 01192318172D          

 30 33  0  0  1  0            999 V2000
   -1.6006    0.3967    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6006    1.2217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8861    1.6342    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1717    1.2217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5428    1.6342    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2965    1.2987    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4680    0.4917    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2750    0.6632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6610    0.3202    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6395   -0.3153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0265   -0.8673    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8485    1.9118    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4360    2.6262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6291    2.4547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0770    3.0678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3320    3.8524    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1389    4.0239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6910    3.4108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8861    2.4592    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3151    1.6342    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3151    2.4592    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0997    2.7142    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5846    2.0467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0997    1.3793    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.3546    0.5947    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1616    0.4231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4165   -0.3615    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7136    1.0362    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6006    2.8717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6006    3.6967    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  3  2  1  0  0  0  0
  3  4  1  1  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  7 10  1  0  0  0  0
 10 11  2  0  0  0  0
  6 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  5 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 13 18  1  0  0  0  0
  3 19  1  0  0  0  0
  2 20  1  0  0  0  0
 21 20  1  1  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 24 23  1  0  0  0  0
 24 20  1  0  0  0  0
 24 25  1  6  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  2  0  0  0  0
 21 29  1  0  0  0  0
 19 29  1  0  0  0  0
 29 30  2  0  0  0  0
M  END


  Mrv2104 01192318172D          

 30 33  0  0  1  0            999 V2000
   -1.6006    0.3967    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6006    1.2217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8861    1.6342    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1717    1.2217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5428    1.6342    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2965    1.2987    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4680    0.4917    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2750    0.6632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6610    0.3202    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6395   -0.3153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0265   -0.8673    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8485    1.9118    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4360    2.6262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6291    2.4547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0770    3.0678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3320    3.8524    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1389    4.0239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6910    3.4108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8861    2.4592    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3151    1.6342    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3151    2.4592    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0997    2.7142    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5846    2.0467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0997    1.3793    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.3546    0.5947    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1616    0.4231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4165   -0.3615    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7136    1.0362    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6006    2.8717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6006    3.6967    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  3  2  1  0  0  0  0
  3  4  1  1  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  7 10  1  0  0  0  0
 10 11  2  0  0  0  0
  6 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  5 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 13 18  1  0  0  0  0
  3 19  1  0  0  0  0
  2 20  1  0  0  0  0
 21 20  1  1  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 24 23  1  0  0  0  0
 24 20  1  0  0  0  0
 24 25  1  6  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  2  0  0  0  0
 21 29  1  0  0  0  0
 19 29  1  0  0  0  0
 29 30  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0350921

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)(C=C)C1=C(C[C@@H]2NC(=O)[C@@H]3CC[C@@H](NC(N)=N)N3C2=O)C2=C(N1)C=CC=C2

> <INCHI_IDENTIFIER>
InChI=1S/C22H28N6O2/c1-4-22(2,3)18-13(12-7-5-6-8-14(12)25-18)11-15-20(30)28-16(19(29)26-15)9-10-17(28)27-21(23)24/h4-8,15-17,25H,1,9-11H2,2-3H3,(H,26,29)(H4,23,24,27)/t15-,16-,17-/m0/s1

> <INCHI_KEY>
WVLIWDCKPOTOKZ-ULQDDVLXSA-N

> <FORMULA>
C22H28N6O2

> <MOLECULAR_WEIGHT>
408.506

> <EXACT_MASS>
408.227374166

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
58

> <JCHEM_AVERAGE_POLARIZABILITY>
44.010516015173295

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
N-[(3S,6S,8aS)-3-{[2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]methyl}-1,4-dioxo-octahydropyrrolo[1,2-a]pyrazin-6-yl]guanidine

> <JCHEM_LOGP>
1.062114261697544

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.4937630169892

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.652299664029862

> <JCHEM_PKA_STRONGEST_BASIC>
11.102552717720748

> <JCHEM_POLAR_SURFACE_AREA>
127.1

> <JCHEM_REFRACTIVITY>
124.69029999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
N-[(3S,6S,8aS)-3-{[2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]methyl}-1,4-dioxo-hexahydropyrrolo[1,2-a]pyrazin-6-yl]guanidine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-JAN-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-JAN-23         0                                  
HETATM    1  O   UNK     0      -2.988   0.741   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.988   2.281   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.654   3.051   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.320   2.281   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.013   3.051   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.420   2.424   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.740   0.918   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.247   1.238   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.234   0.598   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.060  -0.589   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.916  -1.619   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       3.451   3.569   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       2.681   4.902   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.174   4.582   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.144   5.727   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.620   7.191   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.126   7.511   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.156   6.367   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0      -1.654   4.591   0.000  0.00  0.00           N+0
HETATM   20  N   UNK     0      -4.321   3.051   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0      -4.321   4.591   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -5.786   5.066   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -6.691   3.821   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -5.786   2.575   0.000  0.00  0.00           C+0
HETATM   25  N   UNK     0      -6.262   1.110   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0      -7.768   0.790   0.000  0.00  0.00           C+0
HETATM   27  N   UNK     0      -8.244  -0.675   0.000  0.00  0.00           N+0
HETATM   28  N   UNK     0      -8.799   1.934   0.000  0.00  0.00           N+0
HETATM   29  C   UNK     0      -2.988   5.361   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -2.988   6.901   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   20                                                  
CONECT    3    2    4   19                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   14                                                  
CONECT    6    5    7   12                                                  
CONECT    7    6    8    9   10                                             
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    7   11                                                       
CONECT   11   10                                                            
CONECT   12    6   13                                                       
CONECT   13   12   14   18                                                  
CONECT   14   13    5   15                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   13                                                       
CONECT   19    3   29                                                       
CONECT   20    2   21   24                                                  
CONECT   21   20   22   29                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   20   25                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29   21   19   30                                                  
CONECT   30   29                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   66    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₂H₂₈N₆O₂

Average Mass

408.5060 Da

Monoisotopic Mass

408.22737 Da

IUPAC Name

N-[(3S,6S,8aS)-3-{[2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]methyl}-1,4-dioxo-octahydropyrrolo[1,2-a]pyrazin-6-yl]guanidine

Traditional Name

N-[(3S,6S,8aS)-3-{[2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]methyl}-1,4-dioxo-hexahydropyrrolo[1,2-a]pyrazin-6-yl]guanidine

CAS Registry Number

Not Available

SMILES

CC(C)(C=C)C1=C(C[C@@H]2NC(=O)[C@@H]3CC[C@@H](NC(N)=N)N3C2=O)C2=C(N1)C=CC=C2

InChI Identifier

InChI=1S/C22H28N6O2/c1-4-22(2,3)18-13(12-7-5-6-8-14(12)25-18)11-15-20(30)28-16(19(29)26-15)9-10-17(28)27-21(23)24/h4-8,15-17,25H,1,9-11H2,2-3H3,(H,26,29)(H4,23,24,27)/t15-,16-,17-/m0/s1

InChI Key

WVLIWDCKPOTOKZ-ULQDDVLXSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, C2D6OS, experimental)	niwakanji0218@gmail.com	University of California, Los Angeles	Kanji Niwa	2025-04-08	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, C2D6OS, experimental)	niwakanji0218@gmail.com	University of California, Los Angeles	Kanji Niwa	2025-04-08	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, C2D6OS, experimental)	niwakanji0218@gmail.com	University of California, Los Angeles	Kanji Niwa	2025-04-08	View Spectrum
ROESY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, C2D6OS, experimental)	niwakanji0218@gmail.com	University of California, Los Angeles	Kanji Niwa	2025-04-08	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, C2D6OS, experimental)	niwakanji0218@gmail.com	University of California, Los Angeles	Kanji Niwa	2025-04-08	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, C2D6OS, experimental)	niwakanji0218@gmail.com	University of California, Los Angeles	Kanji Niwa	2025-04-08	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, C2D6OS, experimental)	niwakanji0218@gmail.com	University of California, Los Angeles	Kanji Niwa	2025-04-08	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	1.06	ChemAxon
pKa (Strongest Acidic)	11.65	ChemAxon
pKa (Strongest Basic)	11.1	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	127.1 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	124.69 m³·mol⁻¹	ChemAxon
Polarizability	44.01 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

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

Naskar A, Bhanja KK, Roy RK, Patra N: Structural insight into G2019S mutated LRRK2 kinase and brain-penetrant type I inhibitor complex: a molecular dynamics approach. J Biomol Struct Dyn. 2024;42(19):10129-10149. doi: 10.1080/07391102.2023.2255675. Epub 2023 Sep 13. [PubMed:37702159 ]
Rampogu S, Shaik B, Kim JH, Jung TS, Ha MW, Lee KW: Explicit molecular dynamics simulation studies to discover novel natural compound analogues as Mycobacterium tuberculosis inhibitors. Heliyon. 2023 Jan 30;9(2):e13324. doi: 10.1016/j.heliyon.2023.e13324. eCollection 2023 Feb. [PubMed:36816262 ]
Khan S, Fakhar Z, Ahmad A: Targeting ebola virus VP40 protein through novel inhibitors: exploring the structural and dynamic perspectives on molecular landscapes. J Mol Model. 2021 Jan 25;27(2):49. doi: 10.1007/s00894-021-04682-8. [PubMed:33495861 ]
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Showing NP-Card for Comp3 (NP0350921)

MOL for NP0350921 (Comp3)

3D MOL for NP0350921 (Comp3)

3D SDF for NP0350921 (Comp3)

3D-SDF for NP0350921 (Comp3)

PDB for NP0350921 (Comp3)

3D PDB for NP0350921 (Comp3)

SMILES for NP0350921 (Comp3)

INCHI for NP0350921 (Comp3)

Structure for NP0350921 (Comp3)

3D Structure for NP0350921 (Comp3)