NP-MRD: Showing NP-Card for 9-Hydroxyepothilone D (NP0060993)

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Record Information

Version

1.0

Created at

2022-04-28 05:56:02 UTC

Updated at

2022-04-28 05:56:02 UTC

NP-MRD ID

NP0060993

Secondary Accession Numbers

None

Natural Product Identification

Common Name

9-Hydroxyepothilone D

Description

(4S,7R,8S,9S,10R,13Z,16S)-4,8,10-trihydroxy-5,5,7,9,13-pentamethyl-16-[1-(2-methyl-1,3-thiazol-4-yl)prop-1-en-2-yl]-1-oxacyclohexadec-13-ene-2,6-dione belongs to the class of organic compounds known as epothilones and analogues. These are macrolides consisting of a 16-member lactone ring conjugated at the carbon 16 with a 1-(2-methyl-1,3-thiazol-4-yl)prop-1-en-2-yl group. Some epothilone analogues containing a lactam ring instead of the lactone ring. 9-Hydroxyepothilone D is found in Amycolata autotrophica. It was first documented in 2022 (PMID: 35483916). Based on a literature review a significant number of articles have been published on (4S,7R,8S,9S,10R,13Z,16S)-4,8,10-trihydroxy-5,5,7,9,13-pentamethyl-16-[1-(2-methyl-1,3-thiazol-4-yl)prop-1-en-2-yl]-1-oxacyclohexadec-13-ene-2,6-dione (PMID: 35483915) (PMID: 35483914) (PMID: 35483913) (PMID: 35483912).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282207562D          

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M  END

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M  END


  Mrv1652304282207562D          

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 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
  1 18  1  0  0  0  0
 18 19  1  0  0  0  0
 15 20  1  6  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 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
 22 26  2  0  0  0  0
 24 27  1  0  0  0  0
 20 28  1  0  0  0  0
 10 29  1  1  0  0  0
  9 30  1  0  0  0  0
  9 31  1  0  0  0  0
  6 32  1  1  0  0  0
  5 33  1  1  0  0  0
  4 34  1  6  0  0  0
  3 35  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0060993

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1[C@H](O)CC\C(C)=C/C[C@H](OC(=O)C[C@H](O)C(C)(C)C(=O)[C@H](C)[C@H]1O)C(\C)=C\C1=CSC(C)=N1

> <INCHI_IDENTIFIER>
InChI=1S/C27H41NO6S/c1-15-8-10-21(29)17(3)25(32)18(4)26(33)27(6,7)23(30)13-24(31)34-22(11-9-15)16(2)12-20-14-35-19(5)28-20/h9,12,14,17-18,21-23,25,29-30,32H,8,10-11,13H2,1-7H3/b15-9-,16-12+/t17-,18+,21+,22-,23-,25-/m0/s1

> <INCHI_KEY>
VUKFQJGMKMIAMP-VFMZWXMESA-N

> <FORMULA>
C27H41NO6S

> <MOLECULAR_WEIGHT>
507.69

> <EXACT_MASS>
507.265459218

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
55.520508558277555

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S,7R,8S,9S,10R,13Z,16S)-4,8,10-trihydroxy-5,5,7,9,13-pentamethyl-16-[(1E)-1-(2-methyl-1,3-thiazol-4-yl)prop-1-en-2-yl]-1-oxacyclohexadec-13-ene-2,6-dione

> <ALOGPS_LOGP>
3.48

> <JCHEM_LOGP>
3.7511474726666645

> <ALOGPS_LOGS>
-4.99

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.535115000136567

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.969077791481027

> <JCHEM_PKA_STRONGEST_BASIC>
2.726300031921535

> <JCHEM_POLAR_SURFACE_AREA>
116.95000000000002

> <JCHEM_REFRACTIVITY>
137.61380000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.14e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4S,7R,8S,9S,10R,13Z,16S)-4,8,10-trihydroxy-5,5,7,9,13-pentamethyl-16-[(1E)-1-(2-methyl-1,3-thiazol-4-yl)prop-1-en-2-yl]-1-oxacyclohexadec-13-ene-2,6-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       5.137  -0.931   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0       7.914  -7.835   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0       7.438  -9.300   0.000  0.00  0.00           C+0
HETATM   25  S   UNK     0       5.898  -9.300   0.000  0.00  0.00           S+0
HETATM   26  C   UNK     0       5.423  -7.835   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       8.344 -10.546   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       5.945   3.670   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       7.391   3.670   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       2.667   3.080   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2   18                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   35                                                  
CONECT    4    3    5   34                                                  
CONECT    5    4    6   33                                                  
CONECT    6    5    7   32                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   30   31                                             
CONECT   10    9   11   29                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17    1   19                                                  
CONECT   19   18                                                            
CONECT   20   15   21   28                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   26                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   27                                                  
CONECT   25   24   26                                                       
CONECT   26   25   22                                                       
CONECT   27   24                                                            
CONECT   28   20                                                            
CONECT   29   10                                                            
CONECT   30    9                                                            
CONECT   31    9                                                            
CONECT   32    6                                                            
CONECT   33    5                                                            
CONECT   34    4                                                            
CONECT   35    3                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₄₁NO₆S

Average Mass

507.6900 Da

Monoisotopic Mass

507.26546 Da

IUPAC Name

(4S,7R,8S,9S,10R,13Z,16S)-4,8,10-trihydroxy-5,5,7,9,13-pentamethyl-16-[(1E)-1-(2-methyl-1,3-thiazol-4-yl)prop-1-en-2-yl]-1-oxacyclohexadec-13-ene-2,6-dione

Traditional Name

(4S,7R,8S,9S,10R,13Z,16S)-4,8,10-trihydroxy-5,5,7,9,13-pentamethyl-16-[(1E)-1-(2-methyl-1,3-thiazol-4-yl)prop-1-en-2-yl]-1-oxacyclohexadec-13-ene-2,6-dione

CAS Registry Number

Not Available

SMILES

C[C@H]1[C@H](O)CC\C(C)=C/C[C@H](OC(=O)C[C@H](O)C(C)(C)C(=O)[C@H](C)[C@H]1O)C(\C)=C\C1=CSC(C)=N1

InChI Identifier

InChI=1S/C27H41NO6S/c1-15-8-10-21(29)17(3)25(32)18(4)26(33)27(6,7)23(30)13-24(31)34-22(11-9-15)16(2)12-20-14-35-19(5)28-20/h9,12,14,17-18,21-23,25,29-30,32H,8,10-11,13H2,1-7H3/b15-9-,16-12+/t17-,18+,21+,22-,23-,25-/m0/s1

InChI Key

VUKFQJGMKMIAMP-VFMZWXMESA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Pseudonocardia autotrophica	-	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as epothilones and analogues. These are macrolides consisting of a 16-member lactone ring conjugated at the carbon 16 with a 1-(2-methyl-1,3-thiazol-4-yl)prop-1-en-2-yl group. Some epothilone analogues containing a lactam ring instead of the lactone ring.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Macrolides and analogues

Sub Class

Epothilones and analogues

Direct Parent

Epothilones and analogues

Alternative Parents

Substituents

Epothilone
2,4-disubstituted 1,3-thiazole
Heteroaromatic compound
Thiazole
Azole
Cyclic ketone
Secondary alcohol
Lactone
Ketone
Carboxylic acid ester
Oxacycle
Azacycle
Organoheterocyclic compound
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

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	3.48	ALOGPS
logP	3.75	ChemAxon
logS	-5	ALOGPS
pKa (Strongest Acidic)	13.97	ChemAxon
pKa (Strongest Basic)	2.73	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	116.95 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	137.61 m³·mol⁻¹	ChemAxon
Polarizability	55.52 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

163106366

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Uchida Y, Kan H, Sakurai K, Horimoto Y, Hayashi E, Iida A, Okamura N, Oishi K, Matsukawa N: APOE varepsilon4 dose associates with increased brain iron and beta-amyloid via blood-brain barrier dysfunction. J Neurol Neurosurg Psychiatry. 2022 Apr 28. pii: jnnp-2021-328519. doi: 10.1136/jnnp-2021-328519. [PubMed:35483916 ]
Cacciaguerra L, Pagani E, Radaelli M, Mesaros S, Martinelli V, Ivanovic J, Drulovic J, Filippi M, Rocca MA: MR T2-relaxation time as an indirect measure of brain water content and disease activity in NMOSD. J Neurol Neurosurg Psychiatry. 2022 Apr 28. pii: jnnp-2022-328956. doi: 10.1136/jnnp-2022-328956. [PubMed:35483915 ]
Broomfield NM, West R, Barber M, Quinn TJ, Gillespie D, Walters M, House A: TEARS: a longitudinal investigation of the prevalence, psychological associations and trajectory of poststroke emotionalism. J Neurol Neurosurg Psychiatry. 2022 Apr 28. pii: jnnp-2022-329042. doi: 10.1136/jnnp-2022-329042. [PubMed:35483914 ]
Khankari J, Yu Y, Ouyang J, Hussein R, Do HM, Heit JJ, Zaharchuk G: Automated detection of arterial landmarks and vascular occlusions in patients with acute stroke receiving digital subtraction angiography using deep learning. J Neurointerv Surg. 2022 Apr 28. pii: neurintsurg-2021-018638. doi: 10.1136/neurintsurg-2021-018638. [PubMed:35483913 ]
Adeeb N, Dibas M, Diestro JDB, Phan K, Cuellar-Saenz HH, Sweid A, Lay SV, Guenego A, Aslan A, Renieri L, Sundararajan SH, Saliou G, Mohlenbruch M, Regenhardt RW, Vranic JE, Lylyk I, Foreman PM, Vachhani JA, Zupancic V, Hafeez MU, Rutledge C, Waqas M, Tutino VM, Rabinov JD, Ren Y, Schirmer CM, Piano M, Kuhn AL, Michelozzi C, Elens S, Starke RM, Hassan A, Salehani A, Brehm A, MohammedAli M, Jones J, Psychogios M, Spears J, Lubicz B, Panni P, Puri AS, Pero G, Griessenauer CJ, Asadi H, Siddiqui A, Ducruet A, Albuquerque FC, Du R, Kan P, Kalousek V, Lylyk P, Stapleton CJ, Boddu S, Knopman J, Aziz-Sultan MA, Limbucci N, Jabbour P, Cognard C, Patel AB, Dmytriw AA: Comparing treatment outcomes of various intracranial bifurcation aneurysms locations using the Woven EndoBridge (WEB) device. J Neurointerv Surg. 2022 Apr 28. pii: neurintsurg-2022-018694. doi: 10.1136/neurintsurg-2022-018694. [PubMed:35483912 ]

Showing NP-Card for 9-Hydroxyepothilone D (NP0060993)

MOL for NP0060993 (9-Hydroxyepothilone D)

3D MOL for NP0060993 (9-Hydroxyepothilone D)

3D SDF for NP0060993 (9-Hydroxyepothilone D)

3D-SDF for NP0060993 (9-Hydroxyepothilone D)

PDB for NP0060993 (9-Hydroxyepothilone D)

3D PDB for NP0060993 (9-Hydroxyepothilone D)

SMILES for NP0060993 (9-Hydroxyepothilone D)

INCHI for NP0060993 (9-Hydroxyepothilone D)

Structure for NP0060993 (9-Hydroxyepothilone D)

3D Structure for NP0060993 (9-Hydroxyepothilone D)