NP-MRD: Showing NP-Card for 5-Hydroxy-migrastatin (NP0332314)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2024-01-04 04:42:11 UTC

Updated at

2024-09-03 04:18:47 UTC

NP-MRD ID

NP0332314

Natural Product DOI

https://doi.org/10.57994/1516

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5-Hydroxy-migrastatin

Description

5-Hydroxy-migrastatin was first documented in 2023 (PMID: 38093455). Based on a literature review very few articles have been published on 5-Hydroxy-migrastatin.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 01042404422D          

 36 37  0  0  0  0            999 V2000
   -2.8579   -5.7750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -4.5375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -6.6000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9440   -2.6326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 20 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 12 30  1  0  0  0  0
 30 31  1  0  0  0  0
 29 31  1  0  0  0  0
 31 32  2  0  0  0  0
 11 33  1  0  0  0  0
 10 34  2  0  0  0  0
  6 35  1  0  0  0  0
  2 35  1  0  0  0  0
  4 36  2  0  0  0  0
M  END


  Mrv2104 01042404422D          

 36 37  0  0  0  0            999 V2000
   -2.8579   -5.7750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -4.5375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -6.6000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9440   -2.6326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 20 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 12 30  1  0  0  0  0
 30 31  1  0  0  0  0
 29 31  1  0  0  0  0
 31 32  2  0  0  0  0
 11 33  1  0  0  0  0
 10 34  2  0  0  0  0
  6 35  1  0  0  0  0
  2 35  1  0  0  0  0
  4 36  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0332314

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1\C=C\C(O)C\C=C\C(=O)OC(C(C)C(=O)CCCC2CC(=O)NC(=O)C2)\C(C)=C/C(C)C1O

> <INCHI_IDENTIFIER>
InChI=1/C27H39NO8/c1-16-13-17(2)27(18(3)21(30)9-5-7-19-14-23(31)28-24(32)15-19)36-25(33)10-6-8-20(29)11-12-22(35-4)26(16)34/h6,10-13,16,18-20,22,26-27,29,34H,5,7-9,14-15H2,1-4H3,(H,28,31,32)/b10-6+,12-11+,17-13-

> <INCHI_KEY>
KZYPBAIJEAMYNS-XRUINZMDNA-N

> <FORMULA>
C27H39NO8

> <MOLECULAR_WEIGHT>
505.608

> <EXACT_MASS>
505.26756722

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
52.121580840533206

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-{5-[(3Z,8E,12E)-6,10-dihydroxy-7-methoxy-3,5-dimethyl-14-oxo-1-oxacyclotetradeca-3,8,12-trien-2-yl]-4-oxohexyl}piperidine-2,6-dione

> <JCHEM_LOGP>
2.151126181333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.805777238567435

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.796061129331255

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8716635353201605

> <JCHEM_POLAR_SURFACE_AREA>
139.23

> <JCHEM_REFRACTIVITY>
135.62240000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
4-{5-[(3Z,8E,12E)-6,10-dihydroxy-7-methoxy-3,5-dimethyl-14-oxo-1-oxacyclotetradeca-3,8,12-trien-2-yl]-4-oxohexyl}piperidine-2,6-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-JAN-24   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JAN-24         0                                  
HETATM    1  O   UNK     0      -5.335 -10.780   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -5.335  -9.240   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -6.668  -8.470   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -6.668  -6.930   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.335  -6.160   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.667  -6.160   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.000  -6.160   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667  -6.160   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       5.335  -7.700   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       9.336  -6.930   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      10.669  -7.700   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.002  -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       6.668 -11.550   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       8.002 -12.320   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       5.335 -12.320   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       1.334 -10.010   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       1.762  -4.914   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       1.334  -8.470   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      -4.001  -8.470   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -8.002  -6.160   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   35                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   36                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   35                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   34                                                  
CONECT   11   10   12   33                                                  
CONECT   12   11   13   30                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   23                                                  
CONECT   21   20   22                                                       
CONECT   22   21                                                            
CONECT   23   20   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   31                                                       
CONECT   30   12   31                                                       
CONECT   31   30   29   32                                                  
CONECT   32   31                                                            
CONECT   33   11                                                            
CONECT   34   10                                                            
CONECT   35    6    2                                                       
CONECT   36    4                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₉NO₈

Average Mass

505.6080 Da

Monoisotopic Mass

505.26757 Da

IUPAC Name

4-{5-[(3Z,8E,12E)-6,10-dihydroxy-7-methoxy-3,5-dimethyl-14-oxo-1-oxacyclotetradeca-3,8,12-trien-2-yl]-4-oxohexyl}piperidine-2,6-dione

Traditional Name

4-{5-[(3Z,8E,12E)-6,10-dihydroxy-7-methoxy-3,5-dimethyl-14-oxo-1-oxacyclotetradeca-3,8,12-trien-2-yl]-4-oxohexyl}piperidine-2,6-dione

CAS Registry Number

Not Available

SMILES

COC1\C=C\C(O)C\C=C\C(=O)OC(C(C)C(=O)CCCC2CC(=O)NC(=O)C2)\C(C)=C/C(C)C1O

InChI Identifier

InChI=1/C27H39NO8/c1-16-13-17(2)27(18(3)21(30)9-5-7-19-14-23(31)28-24(32)15-19)36-25(33)10-6-8-20(29)11-12-22(35-4)26(16)34/h6,10-13,16,18-20,22,26-27,29,34H,5,7-9,14-15H2,1-4H3,(H,28,31,32)/b10-6+,12-11+,17-13-

InChI Key

KZYPBAIJEAMYNS-XRUINZMDNA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 850 MHz, C2D6OS, experimental)	29cinderella@snu.ac.kr	Not Available	Not Available	2024-05-03	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, 850, C2D6OS, simulated)	29cinderella@snu.ac.kr	Seoul National University	Ji Hyeon Im	2024-05-03	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
cystarginea		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	2.15	ChemAxon
pKa (Strongest Acidic)	11.8	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	139.23 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	135.62 m³·mol⁻¹	ChemAxon
Polarizability	52.12 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	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

Im JH, Oh S, Bae ES, Um S, Lee SK, Ban YH, Oh DC: Discovery and structure elucidation of glycosyl and 5-hydroxy migrastatins from dung beetle gut Kitasatospora sp. J Ind Microbiol Biotechnol. 2023 Feb 17;50(1):kuad046. doi: 10.1093/jimb/kuad046. [PubMed:38093455 ]

Showing NP-Card for 5-Hydroxy-migrastatin (NP0332314)

MOL for NP0332314 (5-Hydroxy-migrastatin)

3D MOL for NP0332314 (5-Hydroxy-migrastatin)

3D SDF for NP0332314 (5-Hydroxy-migrastatin)

3D-SDF for NP0332314 (5-Hydroxy-migrastatin)

PDB for NP0332314 (5-Hydroxy-migrastatin)

3D PDB for NP0332314 (5-Hydroxy-migrastatin)

SMILES for NP0332314 (5-Hydroxy-migrastatin)

INCHI for NP0332314 (5-Hydroxy-migrastatin)

Structure for NP0332314 (5-Hydroxy-migrastatin)

3D Structure for NP0332314 (5-Hydroxy-migrastatin)