NP-MRD: Showing NP-Card for pseudobulbiferamide B (NP0331780)

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Record Information

Version

1.0

Created at

2023-08-25 00:03:03 UTC

Updated at

2024-05-11 02:07:42 UTC

NP-MRD ID

NP0331780

Secondary Accession Numbers

None

Natural Product Identification

Common Name

pseudobulbiferamide B

Description

Not Available

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 08252300032D          

 48 50  0  0  1  0            999 V2000
   -1.4289   -8.2500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -9.4875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -8.2500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5724   -8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -9.4875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -9.9000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579  -10.7250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724  -11.1375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868  -10.7250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -9.9000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 46 47  1  0  0  0  0
 13 48  2  0  0  0  0
M  END


  Mrv2104 08252300032D          

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   -2.1434   -8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -9.4875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -8.2500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0331780

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C30H39N9O8S/c1-2-18(37-30(47)38-20(27(43)44)14-17-8-4-3-5-9-17)24(41)34-15-23(40)35-19(10-6-12-33-29(31)32)26(42)39-13-7-11-22(39)25-36-21(16-48-25)28(45)46/h2-5,8-9,16,19-20,22H,6-7,10-15H2,1H3,(H,34,41)(H,35,40)(H,43,44)(H,45,46)(H4,31,32,33)(H2,37,38,47)/b18-2-/t19-,20-,22-/m0/s1

> <INCHI_KEY>
DKPLZVZSTCYFNW-QTJXMBFXSA-N

> <FORMULA>
C30H39N9O8S

> <MOLECULAR_WEIGHT>
685.76

> <EXACT_MASS>
685.264230426

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
87

> <JCHEM_AVERAGE_POLARIZABILITY>
68.75834535718948

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-2.5402223090139304

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.68162046525058

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.003505897710457

> <JCHEM_PKA_STRONGEST_BASIC>
11.642908674409844

> <JCHEM_POLAR_SURFACE_AREA>
269.03

> <JCHEM_REFRACTIVITY>
183.26530000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
16

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
2-[(2S)-1-[(2S)-5-carbamimidamido-2-{2-[(2Z)-2-({[(1S)-1-carboxy-2-phenylethyl]carbamoyl}amino)but-2-enamido]acetamido}pentanoyl]pyrrolidin-2-yl]-1,3-thiazole-4-carboxylic 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      -2.667 -15.400   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -4.001 -16.170   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -4.001 -17.710   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -5.335 -15.400   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -6.668 -16.170   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -6.668 -17.710   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -5.335 -18.480   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.335 -20.020   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -6.668 -20.790   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -8.002 -20.020   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -8.002 -18.480   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -5.335 -13.860   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      -4.001 -13.090   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      -4.001 -11.550   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      -2.667 -10.780   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  -8.470   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.000  -6.160   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0       0.000  -4.620   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0       1.334  -3.850   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.667  -6.160   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   25  N   UNK     0       4.001  -8.470   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   27  N   UNK     0       6.668  -8.470   0.000  0.00  0.00           N+0
HETATM   28  N   UNK     0       5.335 -10.780   0.000  0.00  0.00           N+0
HETATM   29  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0       2.667  -1.540   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0       2.828  -0.008   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       1.684   1.022   0.000  0.00  0.00           C+0
HETATM   33  N   UNK     0       0.178   0.702   0.000  0.00  0.00           N+0
HETATM   34  C   UNK     0      -0.592   2.036   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -2.124   2.196   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -2.750   3.603   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      -3.029   0.951   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0       0.438   3.180   0.000  0.00  0.00           C+0
HETATM   39  S   UNK     0       1.845   2.554   0.000  0.00  0.00           S+0
HETATM   40  C   UNK     0       4.335   0.312   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       5.105  -1.022   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       4.074  -2.166   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0       0.000  -1.540   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0       1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   45  O   UNK     0      -4.001  -8.470   0.000  0.00  0.00           O+0
HETATM   46  C   UNK     0      -1.334 -11.550   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      -1.334 -13.090   0.000  0.00  0.00           C+0
HETATM   48  O   UNK     0      -2.667 -13.860   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   48                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   46                                                  
CONECT   16   15   17   45                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   44                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   29                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29   21   30   43                                                  
CONECT   30   29   31   42                                                  
CONECT   31   30   32   40                                                  
CONECT   32   31   33   39                                                  
CONECT   33   32   34                                                       
CONECT   34   33   35   38                                                  
CONECT   35   34   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35                                                            
CONECT   38   34   39                                                       
CONECT   39   38   32                                                       
CONECT   40   31   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   30                                                       
CONECT   43   29                                                            
CONECT   44   19                                                            
CONECT   45   16                                                            
CONECT   46   15   47                                                       
CONECT   47   46                                                            
CONECT   48   13                                                            
MASTER        0    0    0    0    0    0    0    0   48    0  100    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₃₉N₉O₈S

Average Mass

685.7600 Da

Monoisotopic Mass

685.26423 Da

IUPAC Name

2-[(2S)-1-[(2S)-5-carbamimidamido-2-{2-[(2Z)-2-({[(1S)-1-carboxy-2-phenylethyl]carbamoyl}amino)but-2-enamido]acetamido}pentanoyl]pyrrolidin-2-yl]-1,3-thiazole-4-carboxylic acid

Traditional Name

2-[(2S)-1-[(2S)-5-carbamimidamido-2-{2-[(2Z)-2-({[(1S)-1-carboxy-2-phenylethyl]carbamoyl}amino)but-2-enamido]acetamido}pentanoyl]pyrrolidin-2-yl]-1,3-thiazole-4-carboxylic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C30H39N9O8S/c1-2-18(37-30(47)38-20(27(43)44)14-17-8-4-3-5-9-17)24(41)34-15-23(40)35-19(10-6-12-33-29(31)32)26(42)39-13-7-11-22(39)25-36-21(16-48-25)28(45)46/h2-5,8-9,16,19-20,22H,6-7,10-15H2,1H3,(H,34,41)(H,35,40)(H,43,44)(H,45,46)(H4,31,32,33)(H2,37,38,47)/b18-2-/t19-,20-,22-/m0/s1

InChI Key

DKPLZVZSTCYFNW-QTJXMBFXSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
ROESY 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
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 700 MHz, C2D6OS, experimental)	wzhong49@gatech.edu	Not Available	Not Available	2023-08-25	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
1D NMR	[¹³C, ] NMR Spectrum (2D, 176 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
ROESY 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
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 700 MHz, C2D6OS, experimental)	wzhong49@gatech.edu	Not Available	Not Available	2023-08-25	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
1D NMR	[¹³C, ] NMR Spectrum (2D, 176 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. MKSA008		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	-2.5	ChemAxon
pKa (Strongest Acidic)	3	ChemAxon
pKa (Strongest Basic)	11.64	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	269.03 Å²	ChemAxon
Rotatable Bond Count	16	ChemAxon
Refractivity	183.27 m³·mol⁻¹	ChemAxon
Polarizability	68.76 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 B (NP0331780)

MOL for NP0331780 (pseudobulbiferamide B)

3D MOL for NP0331780 (pseudobulbiferamide B)

3D SDF for NP0331780 (pseudobulbiferamide B)

3D-SDF for NP0331780 (pseudobulbiferamide B)

PDB for NP0331780 (pseudobulbiferamide B)

3D PDB for NP0331780 (pseudobulbiferamide B)

SMILES for NP0331780 (pseudobulbiferamide B)

INCHI for NP0331780 (pseudobulbiferamide B)

Structure for NP0331780 (pseudobulbiferamide B)

3D Structure for NP0331780 (pseudobulbiferamide B)