NP-MRD: Showing NP-Card for pseudobulbiferamide C (NP0331778)

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Record Information

Version

1.0

Created at

2023-08-25 00:00:37 UTC

Updated at

2024-05-11 02:07:42 UTC

NP-MRD ID

NP0331778

Secondary Accession Numbers

None

Natural Product Identification

Common Name

pseudobulbiferamide C

Description

Not Available

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 08252300002D          

 58 60  0  0  1  0            999 V2000
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M  END


  Mrv2104 08252300002D          

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 13 58  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0331778

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C=C(/NC(=O)N[C@@H](CC1=CC=CC=C1)C(O)=O)C(=O)N[C@@H](C)C(=O)N[C@@H](CCCNC(N)=N)C(=O)N1CCC[C@H]1C1=NC(=CS1)C(=O)N[C@@H](CCC(N)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C36H49N11O10S/c1-3-21(45-36(57)46-24(34(55)56)17-20-9-5-4-6-10-20)29(50)41-19(2)28(49)42-22(11-7-15-40-35(38)39)32(52)47-16-8-12-26(47)31-44-25(18-58-31)30(51)43-23(33(53)54)13-14-27(37)48/h3-6,9-10,18-19,22-24,26H,7-8,11-17H2,1-2H3,(H2,37,48)(H,41,50)(H,42,49)(H,43,51)(H,53,54)(H,55,56)(H4,38,39,40)(H2,45,46,57)/b21-3-/t19-,22-,23-,24-,26-/m0/s1

> <INCHI_KEY>
UONYSWJBINPXCB-GGWFBYQXSA-N

> <FORMULA>
C36H49N11O10S

> <MOLECULAR_WEIGHT>
827.92

> <EXACT_MASS>
827.338457996

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
107

> <JCHEM_AVERAGE_POLARIZABILITY>
81.09414823372231

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-({2-[(2S)-1-[(2S)-5-carbamimidamido-2-[(2S)-2-[(2Z)-2-({[(1S)-1-carboxy-2-phenylethyl]carbamoyl}amino)but-2-enamido]propanamido]pentanoyl]pyrrolidin-2-yl]-1,3-thiazol-4-yl}formamido)-4-carbamoylbutanoic acid

> <JCHEM_LOGP>
-3.6534207564706422

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.5916073002867073

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.920141746211651

> <JCHEM_PKA_STRONGEST_BASIC>
11.541228837875408

> <JCHEM_POLAR_SURFACE_AREA>
341.21999999999997

> <JCHEM_REFRACTIVITY>
217.66920000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
21

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-({2-[(2S)-1-[(2S)-5-carbamimidamido-2-[(2S)-2-[(2Z)-2-({[(1S)-1-carboxy-2-phenylethyl]carbamoyl}amino)but-2-enamido]propanamido]pentanoyl]pyrrolidin-2-yl]-1,3-thiazol-4-yl}formamido)-4-carbamoylbutanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-AUG-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-AUG-23         0                                  
HETATM    1  O   UNK     0      -8.002 -12.320   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -9.336 -11.550   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0     -10.669 -12.320   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -9.336 -10.010   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0     -10.669  -9.240   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0     -12.003 -10.010   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0     -12.003 -11.550   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0     -13.337 -12.320   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0     -14.670 -11.550   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0     -14.670 -10.010   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0     -13.337  -9.240   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -8.002  -9.240   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      -6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      -5.335  -9.240   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      -4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      -1.334 -10.010   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       2.667  -9.240   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0       9.336 -10.010   0.000  0.00  0.00           N+0
HETATM   27  C   UNK     0      10.669  -9.240   0.000  0.00  0.00           C+0
HETATM   28  N   UNK     0      10.669  -7.700   0.000  0.00  0.00           N+0
HETATM   29  N   UNK     0      12.003 -10.010   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0       4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   31  N   UNK     0       5.335 -12.320   0.000  0.00  0.00           N+0
HETATM   32  C   UNK     0       5.496 -13.852   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       4.351 -14.882   0.000  0.00  0.00           C+0
HETATM   34  N   UNK     0       4.512 -16.414   0.000  0.00  0.00           N+0
HETATM   35  C   UNK     0       3.105 -17.040   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       2.785 -18.546   0.000  0.00  0.00           C+0
HETATM   37  N   UNK     0       1.321 -19.022   0.000  0.00  0.00           N+0
HETATM   38  C   UNK     0       1.000 -20.529   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -0.464 -21.004   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -0.784 -22.511   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      -2.249 -22.987   0.000  0.00  0.00           C+0
HETATM   42  N   UNK     0      -2.569 -24.493   0.000  0.00  0.00           N+0
HETATM   43  O   UNK     0      -3.394 -21.956   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0       2.145 -21.559   0.000  0.00  0.00           C+0
HETATM   45  O   UNK     0       1.825 -23.065   0.000  0.00  0.00           O+0
HETATM   46  O   UNK     0       3.609 -21.083   0.000  0.00  0.00           O+0
HETATM   47  O   UNK     0       3.930 -19.577   0.000  0.00  0.00           O+0
HETATM   48  C   UNK     0       2.075 -15.896   0.000  0.00  0.00           C+0
HETATM   49  S   UNK     0       2.845 -14.562   0.000  0.00  0.00           S+0
HETATM   50  C   UNK     0       7.002 -14.172   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0       7.772 -12.838   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0       6.742 -11.694   0.000  0.00  0.00           C+0
HETATM   53  O   UNK     0       2.667 -12.320   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0       1.334 -11.550   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0      -2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   56  C   UNK     0      -4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      -5.335 -12.320   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0      -6.668 -11.550   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   12                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    6                                                       
CONECT   12    4   13                                                       
CONECT   13   12   14   58                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   56                                                  
CONECT   16   15   17   55                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   54                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   30                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30   22   31   53                                                  
CONECT   31   30   32   52                                                  
CONECT   32   31   33   50                                                  
CONECT   33   32   34   49                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36   48                                                  
CONECT   36   35   37   47                                                  
CONECT   37   36   38                                                       
CONECT   38   37   39   44                                                  
CONECT   39   38   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42   43                                                  
CONECT   42   41                                                            
CONECT   43   41                                                            
CONECT   44   38   45   46                                                  
CONECT   45   44                                                            
CONECT   46   44                                                            
CONECT   47   36                                                            
CONECT   48   35   49                                                       
CONECT   49   48   33                                                       
CONECT   50   32   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   31                                                       
CONECT   53   30                                                            
CONECT   54   20                                                            
CONECT   55   16                                                            
CONECT   56   15   57                                                       
CONECT   57   56                                                            
CONECT   58   13                                                            
MASTER        0    0    0    0    0    0    0    0   58    0  120    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₆H₄₉N₁₁O₁₀S

Average Mass

827.9200 Da

Monoisotopic Mass

827.33846 Da

IUPAC Name

(2S)-2-({2-[(2S)-1-[(2S)-5-carbamimidamido-2-[(2S)-2-[(2Z)-2-({[(1S)-1-carboxy-2-phenylethyl]carbamoyl}amino)but-2-enamido]propanamido]pentanoyl]pyrrolidin-2-yl]-1,3-thiazol-4-yl}formamido)-4-carbamoylbutanoic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

C\C=C(/NC(=O)N[C@@H](CC1=CC=CC=C1)C(O)=O)C(=O)N[C@@H](C)C(=O)N[C@@H](CCCNC(N)=N)C(=O)N1CCC[C@H]1C1=NC(=CS1)C(=O)N[C@@H](CCC(N)=O)C(O)=O

InChI Identifier

InChI=1S/C36H49N11O10S/c1-3-21(45-36(57)46-24(34(55)56)17-20-9-5-4-6-10-20)29(50)41-19(2)28(49)42-22(11-7-15-40-35(38)39)32(52)47-16-8-12-26(47)31-44-25(18-58-31)30(51)43-23(33(53)54)13-14-27(37)48/h3-6,9-10,18-19,22-24,26H,7-8,11-17H2,1-2H3,(H2,37,48)(H,41,50)(H,42,49)(H,43,51)(H,53,54)(H,55,56)(H4,38,39,40)(H2,45,46,57)/b21-3-/t19-,22-,23-,24-,26-/m0/s1

InChI Key

UONYSWJBINPXCB-GGWFBYQXSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 700 MHz, C2D6OS, experimental)	wzhong49@gatech.edu	Not Available	Not Available	2023-08-25	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 700 MHz, C2D6OS, experimental)	wzhong49@gatech.edu	Not Available	Not Available	2023-08-25	View Spectrum
ROESY NMR	[¹H, ¹H] NMR Spectrum (2D, 700 MHz, C2D6OS, experimental)	wzhong49@gatech.edu	Not Available	Not Available	2023-08-25	View Spectrum
1D NMR	[¹³C, ] NMR Spectrum (2D, 176 MHz, C2D6OS, experimental)	wzhong49@gatech.edu	Not Available	Not Available	2023-08-25	View Spectrum
FAILED_TO_DETECT NMR	[¹H, ¹H] NMR Spectrum (2D, 700 MHz, C2D6OS, experimental)	wzhong49@gatech.edu	Not Available	Not Available	2023-08-25	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 700 MHz, C2D6OS, experimental)	wzhong49@gatech.edu	Not Available	Not Available	2023-08-25	View Spectrum
1D NMR	[¹H, ] NMR Spectrum (2D, 700 MHz, C2D6OS, experimental)	wzhong49@gatech.edu	Not Available	Not Available	2023-08-25	View Spectrum
1D_DEPT NMR	¹³C NMR Spectrum (1D, 176 MHz, C2D6OS, experimental)	wzhong49@gatech.edu	Not Available	Not Available	2024-05-11	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 700 MHz, C2D6OS, experimental)	wzhong49@gatech.edu	Not Available	Not Available	2023-08-25	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 700 MHz, C2D6OS, experimental)	wzhong49@gatech.edu	Not Available	Not Available	2023-08-25	View Spectrum
1D NMR	[¹³C, ] NMR Spectrum (2D, 176 MHz, C2D6OS, experimental)	wzhong49@gatech.edu	Not Available	Not Available	2023-08-25	View Spectrum
ROESY NMR	[¹H, ¹H] NMR Spectrum (2D, 700 MHz, C2D6OS, experimental)	wzhong49@gatech.edu	Not Available	Not Available	2023-08-25	View Spectrum
FAILED_TO_DETECT NMR	[¹H, ¹H] NMR Spectrum (2D, 700 MHz, C2D6OS, experimental)	wzhong49@gatech.edu	Not Available	Not Available	2023-08-25	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 700 MHz, C2D6OS, experimental)	wzhong49@gatech.edu	Not Available	Not Available	2023-08-25	View Spectrum
1D NMR	[¹H, ] NMR Spectrum (2D, 700 MHz, C2D6OS, experimental)	wzhong49@gatech.edu	Not Available	Not Available	2023-08-25	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
sp. MKSA009		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	-3.7	ChemAxon
pKa (Strongest Acidic)	2.92	ChemAxon
pKa (Strongest Basic)	11.54	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	341.22 Å²	ChemAxon
Rotatable Bond Count	21	ChemAxon
Refractivity	217.67 m³·mol⁻¹	ChemAxon
Polarizability	81.09 Å³	ChemAxon
Number of Rings	3	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

Zhong W, Aiosa N, Deutsch JM, Garg N, Agarwal V: Pseudobulbiferamides: Plasmid-Encoded Ureidopeptide Natural Products with Biosynthetic Gene Clusters Shared Among Marine Bacteria of Different Genera. J Nat Prod. 2023 Oct 27;86(10):2414-2420. doi: 10.1021/acs.jnatprod.3c00595. Epub 2023 Sep 15. [PubMed:37713418 ]

Showing NP-Card for pseudobulbiferamide C (NP0331778)

MOL for NP0331778 (pseudobulbiferamide C)

3D MOL for NP0331778 (pseudobulbiferamide C)

3D SDF for NP0331778 (pseudobulbiferamide C)

3D-SDF for NP0331778 (pseudobulbiferamide C)

PDB for NP0331778 (pseudobulbiferamide C)

3D PDB for NP0331778 (pseudobulbiferamide C)

SMILES for NP0331778 (pseudobulbiferamide C)

INCHI for NP0331778 (pseudobulbiferamide C)

Structure for NP0331778 (pseudobulbiferamide C)

3D Structure for NP0331778 (pseudobulbiferamide C)