NP-MRD: Showing NP-Card for ketomemicin C-418 (NP0350792)

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Record Information

Version

2.0

Created at

2025-03-08 14:45:26 UTC

Updated at

2025-03-21 01:03:16 UTC

NP-MRD ID

NP0350792

Natural Product DOI

https://doi.org/10.57994/3776

Secondary Accession Numbers

None

Natural Product Identification

Common Name

ketomemicin C-418

Description

Based on a literature review very few articles have been published on ketomemicin C-418.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 06052314522D          

 30 30  0  0  1  0            999 V2000
    7.5355   -4.3570    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7429   -4.1282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5447   -3.3273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1484   -4.7002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3466   -5.5011    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.7521   -6.0731    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9595   -5.8443    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7613   -5.0434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3650   -6.4163    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5724   -6.1875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9779   -6.7595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1852   -6.5307    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1760   -7.5604    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5631   -7.2172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9687   -7.7892    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3558   -7.4460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1392   -5.7299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3374   -6.5307    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7337   -5.1578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5263   -5.3867    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.1208   -4.8146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9134   -5.0434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5079   -4.4714    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3005   -4.7002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4987   -5.5011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9042   -6.0731    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1116   -5.8443    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7245   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5171   -6.4163    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1300   -6.7595    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  5  4  1  0  0  0  0
  5  6  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  9  7  1  0  0  0  0
  9 10  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
  9 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
  5 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 20 19  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 22 27  1  0  0  0  0
 20 28  1  0  0  0  0
 28 29  2  0  0  0  0
 28 30  1  0  0  0  0
M  END


  Mrv2104 06052314522D          

 30 30  0  0  1  0            999 V2000
    7.5355   -4.3570    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7429   -4.1282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5447   -3.3273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1484   -4.7002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3466   -5.5011    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.7521   -6.0731    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9595   -5.8443    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7613   -5.0434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3650   -6.4163    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5724   -6.1875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9779   -6.7595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1852   -6.5307    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1760   -7.5604    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5631   -7.2172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9687   -7.7892    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3558   -7.4460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1392   -5.7299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3374   -6.5307    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7337   -5.1578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5263   -5.3867    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.1208   -4.8146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9134   -5.0434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5079   -4.4714    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3005   -4.7002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4987   -5.5011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9042   -6.0731    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1116   -5.8443    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7245   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5171   -6.4163    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1300   -6.7595    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  5  4  1  0  0  0  0
  5  6  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  9  7  1  0  0  0  0
  9 10  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
  9 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
  5 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 20 19  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 22 27  1  0  0  0  0
 20 28  1  0  0  0  0
 28 29  2  0  0  0  0
 28 30  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0350792

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)C[C@@H](NC(=O)[C@@H](NC(N)=N)C(C)C)C(=O)C[C@@H](CC1=CC=CC=C1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C22H34N4O4/c1-13(2)10-17(25-20(28)19(14(3)4)26-22(23)24)18(27)12-16(21(29)30)11-15-8-6-5-7-9-15/h5-9,13-14,16-17,19H,10-12H2,1-4H3,(H,25,28)(H,29,30)(H4,23,24,26)/t16-,17-,19+/m1/s1

> <INCHI_KEY>
YMBMEDYEBLNAHH-LMMKCTJWSA-N

> <FORMULA>
C22H34N4O4

> <MOLECULAR_WEIGHT>
418.538

> <EXACT_MASS>
418.258005591

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
45.426077410938525

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R,5R)-2-benzyl-5-[(2S)-2-carbamimidamido-3-methylbutanamido]-7-methyl-4-oxooctanoic acid

> <JCHEM_LOGP>
1.323234781125899

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.024586938247406

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.058064185456498

> <JCHEM_PKA_STRONGEST_BASIC>
11.232712532998322

> <JCHEM_POLAR_SURFACE_AREA>
145.36999999999998

> <JCHEM_REFRACTIVITY>
124.89339999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,5R)-2-benzyl-5-[(2S)-2-carbamimidamido-3-methylbutanamido]-7-methyl-4-oxooctanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-JUN-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-JUN-23         0                                  
HETATM    1  C   UNK     0      14.066  -8.133   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.587  -7.706   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      12.217  -6.211   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      11.477  -8.774   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      11.847 -10.269   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      10.737 -11.336   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       9.258 -10.909   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       8.888  -9.414   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       8.148 -11.977   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       6.668 -11.550   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       5.559 -12.618   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       4.079 -12.191   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       5.929 -14.113   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       8.518 -13.472   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.408 -14.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.997 -13.899   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      13.327 -10.696   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      13.696 -12.191   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      14.436  -9.628   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      15.916 -10.055   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      17.025  -8.987   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      18.505  -9.414   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      19.615  -8.347   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      21.094  -8.774   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      21.464 -10.269   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      20.355 -11.336   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      18.875 -10.909   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      16.286 -11.550   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      17.765 -11.977   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      15.176 -12.618   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6   17                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14    9   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17    5   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21   28                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   27                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   22                                                       
CONECT   28   20   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   60    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₂H₃₄N₄O₄

Average Mass

418.5380 Da

Monoisotopic Mass

418.25801 Da

IUPAC Name

(2R,5R)-2-benzyl-5-[(2S)-2-carbamimidamido-3-methylbutanamido]-7-methyl-4-oxooctanoic acid

Traditional Name

(2R,5R)-2-benzyl-5-[(2S)-2-carbamimidamido-3-methylbutanamido]-7-methyl-4-oxooctanoic acid

CAS Registry Number

Not Available

SMILES

CC(C)C[C@@H](NC(=O)[C@@H](NC(N)=N)C(C)C)C(=O)C[C@@H](CC1=CC=CC=C1)C(O)=O

InChI Identifier

InChI=1S/C22H34N4O4/c1-13(2)10-17(25-20(28)19(14(3)4)26-22(23)24)18(27)12-16(21(29)30)11-15-8-6-5-7-9-15/h5-9,13-14,16-17,19H,10-12H2,1-4H3,(H,25,28)(H,29,30)(H4,23,24,26)/t16-,17-,19+/m1/s1

InChI Key

YMBMEDYEBLNAHH-LMMKCTJWSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 599 MHz, CD3OD, experimental)	g6castro@ucsd.edu	University of California San Diego	Gabriel Castro-Falcón	2025-03-08	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 599 MHz, CD3OD, experimental)	g6castro@ucsd.edu	University of California San Diego	Gabriel Castro-Falcón	2025-03-08	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 599 MHz, CD3OD, experimental)	g6castro@ucsd.edu	University of California San Diego	Gabriel Castro-Falcón	2025-03-08	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 599 MHz, CD3OD, experimental)	g6castro@ucsd.edu	University of California San Diego	Gabriel Castro-Falcón	2025-03-08	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 599.109996545 MHz, CD₃OD, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 599.109996545, CD₃OD, simulated)	g6castro@ucsd.edu	University of California San Diego	Gabriel Castro-Falcón	2025-03-08	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Salinispora pacifica		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	1.32	ChemAxon
pKa (Strongest Acidic)	4.06	ChemAxon
pKa (Strongest Basic)	11.23	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	145.37 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	124.89 m³·mol⁻¹	ChemAxon
Polarizability	45.43 Å³	ChemAxon
Number of Rings	1	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

Showing NP-Card for ketomemicin C-418 (NP0350792)

MOL for NP0350792 (ketomemicin C-418)

3D MOL for NP0350792 (ketomemicin C-418)

3D SDF for NP0350792 (ketomemicin C-418)

3D-SDF for NP0350792 (ketomemicin C-418)

PDB for NP0350792 (ketomemicin C-418)

3D PDB for NP0350792 (ketomemicin C-418)

SMILES for NP0350792 (ketomemicin C-418)

INCHI for NP0350792 (ketomemicin C-418)

Structure for NP0350792 (ketomemicin C-418)

3D Structure for NP0350792 (ketomemicin C-418)