NP-MRD: Showing NP-Card for Homomorphin A (NP0333323)

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Record Information

Version

2.0

Created at

2024-05-30 14:45:13 UTC

Updated at

2024-11-01 00:37:24 UTC

NP-MRD ID

NP0333323

Natural Product DOI

https://doi.org/10.57994/2681

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Homomorphin A

Description

Homomorphin A belongs to the class of organic compounds known as indoles. Indoles are compounds containing an indole moiety, which consists of pyrrole ring fused to benzene to form 2,3-benzopyrrole. Based on a literature review very few articles have been published on Homomorphin A.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 02112317212D          

 24 26  0  0  1  0            999 V2000
    0.3739   -3.7192    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1809   -3.5477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4358   -2.7631    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2428   -2.5916    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6288   -2.9346    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    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   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7329   -4.1608    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5399   -3.9893    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0919   -4.6024    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8989   -4.4309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8370   -5.3870    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3890   -6.0001    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2849   -4.7739    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7948   -3.2047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6018   -3.0331    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  0  0  0  0
  3  5  1  1  0  0  0
  3  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
  7 15  1  0  0  0  0
 10 15  1  0  0  0  0
  2 16  1  0  0  0  0
 17 16  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  6  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 17 22  1  1  0  0  0
 17 23  1  0  0  0  0
  4 23  1  0  0  0  0
 23 24  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0333323

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]1(CC2=CNC3=CC=CC=C23)NC(=O)[C@@]([H])(NC1=O)[C@H](C)CC

> <INCHI_IDENTIFIER>
InChI=1S/C17H21N3O2/c1-3-10(2)15-17(22)19-14(16(21)20-15)8-11-9-18-13-7-5-4-6-12(11)13/h4-7,9-10,14-15,18H,3,8H2,1-2H3,(H,19,22)(H,20,21)/t10-,14+,15+/m1/s1

> <INCHI_KEY>
PGCNHGBQEYFZEX-ONERCXAPSA-N

> <FORMULA>
C17H21N3O2

> <MOLECULAR_WEIGHT>
299.374

> <EXACT_MASS>
299.163376928

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
31.21669409835919

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S,6S)-3-[(2R)-butan-2-yl]-6-[(1H-indol-3-yl)methyl]piperazine-2,5-dione

> <JCHEM_LOGP>
2.014114252333332

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.308800050089989

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.228294091542487

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7610856097863246

> <JCHEM_POLAR_SURFACE_AREA>
73.99000000000001

> <JCHEM_REFRACTIVITY>
83.8969

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6S)-3-[(2R)-butan-2-yl]-6-(1H-indol-3-ylmethyl)piperazine-2,5-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-FEB-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-FEB-23         0                                  
HETATM    1  O   UNK     0       0.698  -6.943   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.204  -6.622   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.680  -5.158   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       4.187  -4.838   0.000  0.00  0.00           N+0
HETATM    5  H   UNK     0       1.174  -5.478   0.000  0.00  0.00           H+0
HETATM    6  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       3.235  -7.767   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       4.741  -7.447   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.772  -8.591   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.278  -8.271   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.296 -10.056   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.326 -11.200   0.000  0.00  0.00           C+0
HETATM   22  H   UNK     0       4.265  -8.911   0.000  0.00  0.00           H+0
HETATM   23  C   UNK     0       5.217  -5.982   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       6.723  -5.662   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   16                                                  
CONECT    3    2    4    5    6                                             
CONECT    4    3   23                                                       
CONECT    5    3                                                            
CONECT    6    3    7                                                       
CONECT    7    6    8   15                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14    7   10                                                  
CONECT   16    2   17                                                       
CONECT   17   16   18   22   23                                             
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20                                                            
CONECT   22   17                                                            
CONECT   23   17    4   24                                                  
CONECT   24   23                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   52    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₇H₂₁N₃O₂

Average Mass

299.3740 Da

Monoisotopic Mass

299.16338 Da

IUPAC Name

(3S,6S)-3-[(2R)-butan-2-yl]-6-[(1H-indol-3-yl)methyl]piperazine-2,5-dione

Traditional Name

(3S,6S)-3-[(2R)-butan-2-yl]-6-(1H-indol-3-ylmethyl)piperazine-2,5-dione

CAS Registry Number

Not Available

SMILES

[H][C@@]1(CC2=CNC3=CC=CC=C23)NC(=O)[C@@]([H])(NC1=O)[C@H](C)CC

InChI Identifier

InChI=1S/C17H21N3O2/c1-3-10(2)15-17(22)19-14(16(21)20-15)8-11-9-18-13-7-5-4-6-12(11)13/h4-7,9-10,14-15,18H,3,8H2,1-2H3,(H,19,22)(H,20,21)/t10-,14+,15+/m1/s1

InChI Key

PGCNHGBQEYFZEX-ONERCXAPSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 400 MHz, CD3OD, experimental)	shuyilin@usc.edu	University of Southern California	Shu-Yi Lin	2024-05-30	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 400 MHz, CD3OD, experimental)	shuyilin@usc.edu	University of Southern California	Shu-Yi Lin	2024-05-30	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 400 MHz, CD3OD, experimental)	shuyilin@usc.edu	University of Southern California	Shu-Yi Lin	2024-05-30	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 400 MHz, CD3OD, experimental)	shuyilin@usc.edu	University of Southern California	Shu-Yi Lin	2024-05-30	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, CD3OD, experimental)	shuyilin@usc.edu	University of Southern California	Shu-Yi Lin	2024-05-30	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CD3OD, experimental)	shuyilin@usc.edu	University of Southern California	Shu-Yi Lin	2024-05-30	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 400.067164092, CD₃OD, simulated)	shuyilin@usc.edu	University of Southern California	Shu-Yi Lin	2024-05-30	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
homomorphus		Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as indoles. Indoles are compounds containing an indole moiety, which consists of pyrrole ring fused to benzene to form 2,3-benzopyrrole.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indoles

Direct Parent

Indoles

Alternative Parents

Substituents

Indole
Benzenoid
Heteroaromatic compound
Cyclic carboximidic acid
Pyrrole
Azacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboximidic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen 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	2.01	ChemAxon
pKa (Strongest Acidic)	11.23	ChemAxon
pKa (Strongest Basic)	-3.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	73.99 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	83.9 m³·mol⁻¹	ChemAxon
Polarizability	31.22 Å³	ChemAxon
Number of Rings	3	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

Not Available

Showing NP-Card for Homomorphin A (NP0333323)

MOL for NP0333323 (Homomorphin A)

3D MOL for NP0333323 (Homomorphin A)

3D SDF for NP0333323 (Homomorphin A)

3D-SDF for NP0333323 (Homomorphin A)

PDB for NP0333323 (Homomorphin A)

3D PDB for NP0333323 (Homomorphin A)

SMILES for NP0333323 (Homomorphin A)

INCHI for NP0333323 (Homomorphin A)

Structure for NP0333323 (Homomorphin A)

3D Structure for NP0333323 (Homomorphin A)