NP-MRD: Showing NP-Card for Arabipeptin A (NP0331570)

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Record Information

Version

2.0

Created at

2023-03-21 20:00:13 UTC

Updated at

2026-02-25 16:03:28 UTC

NP-MRD ID

NP0331570

Natural Product DOI

https://doi.org/10.57994/0549

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Arabipeptin A

Description

Arabipeptin A was first documented in 2023 (PMID: 36529706).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309122219452D          

 52 56  0  0  1  0            999 V2000
   -0.4208   -5.0925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0934   -4.6148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8435   -4.9584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0160   -3.7934    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8256   -3.5689    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4416   -2.9394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  9 51  1  0  0  0  0
 51 52  2  0  0  0  0
  6 52  1  0  0  0  0
M  END


  Mrv1652309122219452D          

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  6 52  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0331570

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)[C@@H]1OC2=CC=C(C[C@H](NC(=O)CNC(=O)[C@H](CC3=CNC4=C3C=CC=C4)NC(=O)[C@H]1NC(=O)[C@H](CC1=CC=CC=C1)N(C)C)C(O)=O)C=C2

> <INCHI_IDENTIFIER>
InChI=1S/C39H46N6O7/c1-23(2)35-34(44-37(48)32(45(3)4)19-24-10-6-5-7-11-24)38(49)43-30(20-26-21-40-29-13-9-8-12-28(26)29)36(47)41-22-33(46)42-31(39(50)51)18-25-14-16-27(52-35)17-15-25/h5-17,21,23,30-32,34-35,40H,18-20,22H2,1-4H3,(H,41,47)(H,42,46)(H,43,49)(H,44,48)(H,50,51)/t30-,31-,32-,34-,35-/m0/s1

> <INCHI_KEY>
QJWNAJPBUOFEQC-SEVYIBDJSA-N

> <FORMULA>
C39H46N6O7

> <MOLECULAR_WEIGHT>
710.832

> <EXACT_MASS>
710.342797845

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
98

> <JCHEM_AVERAGE_POLARIZABILITY>
75.26220600982325

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4S,7S,13S)-4-[(2S)-2-(dimethylamino)-3-phenylpropanamido]-7-[(1H-indol-3-yl)methyl]-5,8,11-trioxo-3-(propan-2-yl)-2-oxa-6,9,12-triazabicyclo[13.2.2]nonadeca-1(17),15,18-triene-13-carboxylic acid

> <JCHEM_LOGP>
0.48954348210292814

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.912020985497973

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.188159038080406

> <JCHEM_PKA_STRONGEST_BASIC>
7.241462842422307

> <JCHEM_POLAR_SURFACE_AREA>
181.95999999999998

> <JCHEM_REFRACTIVITY>
193.36579999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(3S,4S,7S,13S)-4-[(2S)-2-(dimethylamino)-3-phenylpropanamido]-7-(1H-indol-3-ylmethyl)-3-isopropyl-5,8,11-trioxo-2-oxa-6,9,12-triazabicyclo[13.2.2]nonadeca-1(17),15,18-triene-13-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0      -0.786  -9.506   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.041  -8.614   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.441  -9.256   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.896  -7.081   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -3.408  -6.662   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -4.558  -5.487   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.357  -4.476   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.539  -2.960   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.910  -2.257   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.326  -0.717   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.390   0.569   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -1.884   1.246   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      -0.257   1.186   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       0.123   2.679   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       1.229   0.448   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       2.240  -0.721   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       2.765  -2.181   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.285  -1.936   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       2.726  -3.732   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.233  -4.052   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.709  -5.516   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.803  -6.762   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0       4.709  -8.008   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0       6.173  -7.532   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.173  -5.992   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       7.507  -5.222   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       8.841  -5.992   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       8.841  -7.532   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       7.507  -8.302   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0       2.131  -5.163   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0       1.062  -6.282   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       1.967  -7.528   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -0.332  -6.952   0.000  0.00  0.00           C+0
HETATM   34  N   UNK     0       0.071  -8.438   0.000  0.00  0.00           N+0
HETATM   35  C   UNK     0       1.560  -8.831   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       2.645  -7.739   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       1.964 -10.318   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       3.453 -10.711   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       3.856 -12.197   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       5.345 -12.591   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       5.749 -14.077   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       4.664 -15.170   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       3.175 -14.776   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       2.771 -13.290   0.000  0.00  0.00           C+0
HETATM   45  N   UNK     0       0.879 -11.410   0.000  0.00  0.00           N+0
HETATM   46  C   UNK     0       1.282 -12.896   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      -0.610 -11.017   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      -4.360   1.765   0.000  0.00  0.00           C+0
HETATM   49  O   UNK     0      -5.881   1.522   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      -3.810   3.203   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0      -6.100  -3.275   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      -5.964  -4.796   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   33                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   52                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   51                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   48                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   30                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   25                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   29                                                  
CONECT   25   24   21   26                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   24                                                       
CONECT   30   19   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31    4   34                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   38   45                                                  
CONECT   38   37   39                                                       
CONECT   39   38   40   44                                                  
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   39                                                       
CONECT   45   37   46   47                                                  
CONECT   46   45                                                            
CONECT   47   45                                                            
CONECT   48   11   49   50                                                  
CONECT   49   48                                                            
CONECT   50   48                                                            
CONECT   51    9   52                                                       
CONECT   52   51    6                                                       
MASTER        0    0    0    0    0    0    0    0   52    0  112    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₉H₄₆N₆O₇

Average Mass

710.8320 Da

Monoisotopic Mass

710.34280 Da

IUPAC Name

(3S,4S,7S,13S)-4-[(2S)-2-(dimethylamino)-3-phenylpropanamido]-7-[(1H-indol-3-yl)methyl]-5,8,11-trioxo-3-(propan-2-yl)-2-oxa-6,9,12-triazabicyclo[13.2.2]nonadeca-1(17),15,18-triene-13-carboxylic acid

Traditional Name

(3S,4S,7S,13S)-4-[(2S)-2-(dimethylamino)-3-phenylpropanamido]-7-(1H-indol-3-ylmethyl)-3-isopropyl-5,8,11-trioxo-2-oxa-6,9,12-triazabicyclo[13.2.2]nonadeca-1(17),15,18-triene-13-carboxylic acid

CAS Registry Number

Not Available

SMILES

CC(C)[C@@H]1OC2=CC=C(C[C@H](NC(=O)CNC(=O)[C@H](CC3=CNC4=C3C=CC=C4)NC(=O)[C@H]1NC(=O)[C@H](CC1=CC=CC=C1)N(C)C)C(O)=O)C=C2

InChI Identifier

InChI=1S/C39H46N6O7/c1-23(2)35-34(44-37(48)32(45(3)4)19-24-10-6-5-7-11-24)38(49)43-30(20-26-21-40-29-13-9-8-12-28(26)29)36(47)41-22-33(46)42-31(39(50)51)18-25-14-16-27(52-35)17-15-25/h5-17,21,23,30-32,34-35,40H,18-20,22H2,1-4H3,(H,41,47)(H,42,46)(H,43,49)(H,44,48)(H,50,51)/t30-,31-,32-,34-,35-/m0/s1

InChI Key

QJWNAJPBUOFEQC-SEVYIBDJSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
TOCSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CH3OH, experimental)	[email protected]	Not Available	Not Available	2023-03-23	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CH3OH, experimental)	[email protected]	Not Available	Not Available	2023-03-23	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 126 MHz, CH3OH, experimental)	[email protected]	Not Available	Not Available	2023-03-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CH3OH, experimental)	[email protected]	Not Available	Not Available	2023-03-23	View Spectrum
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CH3OH, experimental)	[email protected]	Not Available	Not Available	2023-03-23	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 126 MHz, CH3OH, experimental)	[email protected]	Not Available	Not Available	2023-03-23	View Spectrum
TOCSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, FAILED_TO_DETECT, experimental)	[email protected]	Not Available	Not Available	2023-03-21	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, FAILED_TO_DETECT, experimental)	[email protected]	Not Available	Not Available	2023-03-21	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 126 MHz, FAILED_TO_DETECT, experimental)	[email protected]	Not Available	Not Available	2023-03-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, FAILED_TO_DETECT, experimental)	[email protected]	Not Available	Not Available	2023-03-21	View Spectrum
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, FAILED_TO_DETECT, experimental)	[email protected]	Not Available	Not Available	2023-03-21	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 126 MHz, FAILED_TO_DETECT, experimental)	[email protected]	Not Available	Not Available	2023-03-21	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, 500.0, Methanol-d4, simulated)	[email protected]	Not Available	Not Available	2026-02-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 125.0, Methanol-d4, simulated)	[email protected]	Not Available	Not Available	2026-02-25	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Coffea arabica		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	0.49	ChemAxon
pKa (Strongest Acidic)	3.19	ChemAxon
pKa (Strongest Basic)	7.24	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	181.96 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	193.37 m³·mol⁻¹	ChemAxon
Polarizability	75.26 Å³	ChemAxon
Number of Rings	5	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

Not Available

References

General References

DOI: 10.1002/anie.202218082

Showing NP-Card for Arabipeptin A (NP0331570)

MOL for NP0331570 (Arabipeptin A)

3D MOL for NP0331570 (Arabipeptin A)

3D SDF for NP0331570 (Arabipeptin A)

3D-SDF for NP0331570 (Arabipeptin A)

PDB for NP0331570 (Arabipeptin A)

3D PDB for NP0331570 (Arabipeptin A)

SMILES for NP0331570 (Arabipeptin A)

INCHI for NP0331570 (Arabipeptin A)

Structure for NP0331570 (Arabipeptin A)

3D Structure for NP0331570 (Arabipeptin A)