NP-MRD: Showing NP-Card for 8''-Hydroxypactamycin (NP0061954)

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Record Information

Version

2.0

Created at

2022-04-28 06:38:47 UTC

Updated at

2022-04-28 06:38:47 UTC

NP-MRD ID

NP0061954

Secondary Accession Numbers

None

Natural Product Identification

Common Name

8''-Hydroxypactamycin

Description

8''-Hydroxypactamycin belongs to the class of organic compounds known as alkyl-phenylketones. These are aromatic compounds containing a ketone substituted by one alkyl group, and a phenyl group. 8''-Hydroxypactamycin is found in Streptomyces sp. WP-4371. 8''-Hydroxypactamycin was first documented in 1986 (PMID: 3818452). Based on a literature review very few articles have been published on 8''-Hydroxypactamycin.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282208382D          

 41 43  0  0  1  0            999 V2000
    5.7920   -4.6759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0074   -4.9308    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.9635   -3.8689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9527   -3.0198    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1681   -3.2747    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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 40 41  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304282208382D          

 41 43  0  0  1  0            999 V2000
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    1.9933   -4.8788    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6557   -5.3707    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4128   -5.0431    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5608   -6.1903    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2232   -6.6822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8037   -6.5179    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3981   -4.7268    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8358   -5.7378    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0512   -5.9927    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4489   -6.2898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2336   -6.0349    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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  4  7  1  0  0  0  0
  8  7  1  1  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
  8 12  1  0  0  0  0
 12 13  1  1  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 17 22  1  0  0  0  0
 22 23  1  0  0  0  0
 18 24  1  0  0  0  0
 12 25  1  6  0  0  0
 11 26  1  1  0  0  0
 11 27  1  6  0  0  0
 10 28  1  1  0  0  0
 28 29  1  0  0  0  0
 28 30  1  1  0  0  0
 10 31  1  6  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
 34 35  1  0  0  0  0
 34 36  1  0  0  0  0
  9 37  1  6  0  0  0
  2 38  1  0  0  0  0
 38 39  2  0  0  0  0
 38 40  1  0  0  0  0
 40 41  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0061954

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](O)[C@]1(NC(=O)N(C)C)[C@@H](N)[C@H](NC2=CC(=CC=C2)C(=O)CO)[C@](O)(COC(=O)C2=C(O)C=CC=C2C)[C@]1(C)O

> <INCHI_IDENTIFIER>
InChI=1S/C28H38N4O9/c1-15-8-6-11-19(35)21(15)24(37)41-14-27(40)23(30-18-10-7-9-17(12-18)20(36)13-33)22(29)28(16(2)34,26(27,3)39)31-25(38)32(4)5/h6-12,16,22-23,30,33-35,39-40H,13-14,29H2,1-5H3,(H,31,38)/t16-,22-,23-,26-,27+,28-/m0/s1

> <INCHI_KEY>
REZOEBXINKYJRQ-WCINKGOFSA-N

> <FORMULA>
C28H38N4O9

> <MOLECULAR_WEIGHT>
574.631

> <EXACT_MASS>
574.26387882

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
79

> <JCHEM_AVERAGE_POLARIZABILITY>
58.856019052747754

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(1S,2R,3R,4S,5S)-4-amino-3-[(dimethylcarbamoyl)amino]-1,2-dihydroxy-5-{[3-(2-hydroxyacetyl)phenyl]amino}-3-[(1S)-1-hydroxyethyl]-2-methylcyclopentyl]methyl 2-hydroxy-6-methylbenzoate

> <ALOGPS_LOGP>
0.52

> <JCHEM_LOGP>
-0.20814360533333293

> <ALOGPS_LOGS>
-2.79

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.180171083825813

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.856538783971674

> <JCHEM_PKA_STRONGEST_BASIC>
7.632448463925371

> <JCHEM_POLAR_SURFACE_AREA>
214.91

> <JCHEM_REFRACTIVITY>
149.4018

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.42e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(1S,2R,3R,4S,5S)-4-amino-3-[(dimethylcarbamoyl)amino]-1,2-dihydroxy-5-{[3-(2-hydroxyacetyl)phenyl]amino}-3-[(1S)-1-hydroxyethyl]-2-methylcyclopentyl]methyl 2-hydroxy-6-methylbenzoate

> <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      10.812  -8.728   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.347  -9.204   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.203  -8.174   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.523  -6.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.987  -6.191   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.132  -7.222   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       7.378  -5.637   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       5.914  -6.113   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.438  -7.577   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.898  -7.577   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.422  -6.113   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.668  -5.208   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.912  -3.866   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       4.696  -2.540   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       3.940  -1.199   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       2.400  -1.183   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       4.724   0.127   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.968   1.469   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.752   2.794   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.292   2.778   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.048   1.436   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.264   0.111   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       7.020  -1.231   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       2.428   1.485   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       5.424  -3.866   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       2.380  -4.979   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       1.912  -6.417   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.498  -8.218   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.242  -7.326   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       2.353  -9.752   0.000  0.00  0.00           O+0
HETATM   31  N   UNK     0       3.721  -9.107   0.000  0.00  0.00           N+0
HETATM   32  C   UNK     0       4.957 -10.025   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       6.371  -9.414   0.000  0.00  0.00           O+0
HETATM   34  N   UNK     0       4.780 -11.555   0.000  0.00  0.00           N+0
HETATM   35  C   UNK     0       6.017 -12.473   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       3.367 -12.167   0.000  0.00  0.00           C+0
HETATM   37  N   UNK     0       6.343  -8.823   0.000  0.00  0.00           N+0
HETATM   38  C   UNK     0       9.027 -10.710   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0       7.562 -11.186   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      10.171 -11.741   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      11.636 -11.265   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   38                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    7                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
CONECT    7    4    8                                                       
CONECT    8    7    9   12                                                  
CONECT    9    8   10   37                                                  
CONECT   10    9   11   28   31                                             
CONECT   11   10   12   26   27                                             
CONECT   12   11    8   13   25                                             
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   22                                                  
CONECT   18   17   19   24                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   17   23                                                  
CONECT   23   22                                                            
CONECT   24   18                                                            
CONECT   25   12                                                            
CONECT   26   11                                                            
CONECT   27   11                                                            
CONECT   28   10   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28                                                            
CONECT   31   10   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34                                                            
CONECT   37    9                                                            
CONECT   38    2   39   40                                                  
CONECT   39   38                                                            
CONECT   40   38   41                                                       
CONECT   41   40                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   86    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₈N₄O₉

Average Mass

574.6310 Da

Monoisotopic Mass

574.26388 Da

IUPAC Name

[(1S,2R,3R,4S,5S)-4-amino-3-[(dimethylcarbamoyl)amino]-1,2-dihydroxy-5-{[3-(2-hydroxyacetyl)phenyl]amino}-3-[(1S)-1-hydroxyethyl]-2-methylcyclopentyl]methyl 2-hydroxy-6-methylbenzoate

Traditional Name

[(1S,2R,3R,4S,5S)-4-amino-3-[(dimethylcarbamoyl)amino]-1,2-dihydroxy-5-{[3-(2-hydroxyacetyl)phenyl]amino}-3-[(1S)-1-hydroxyethyl]-2-methylcyclopentyl]methyl 2-hydroxy-6-methylbenzoate

CAS Registry Number

Not Available

SMILES

C[C@H](O)[C@]1(NC(=O)N(C)C)[C@@H](N)[C@H](NC2=CC(=CC=C2)C(=O)CO)[C@](O)(COC(=O)C2=C(O)C=CC=C2C)[C@]1(C)O

InChI Identifier

InChI=1S/C28H38N4O9/c1-15-8-6-11-19(35)21(15)24(37)41-14-27(40)23(30-18-10-7-9-17(12-18)20(36)13-33)22(29)28(16(2)34,26(27,3)39)31-25(38)32(4)5/h6-12,16,22-23,30,33-35,39-40H,13-14,29H2,1-5H3,(H,31,38)/t16-,22-,23-,26-,27+,28-/m0/s1

InChI Key

REZOEBXINKYJRQ-WCINKGOFSA-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
Streptomyces sp. WP-4371	Bacteria	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alkyl-phenylketones. These are aromatic compounds containing a ketone substituted by one alkyl group, and a phenyl group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Alkyl-phenylketones

Alternative Parents

Substituents

Alkyl-phenylketone
O-hydroxybenzoic acid ester
Aromatic monoterpenoid
Salicylic acid or derivatives
Monoterpenoid
Benzoate ester
Monocyclic monoterpenoid
11-noriridane monoterpenoid
Benzoic acid or derivatives
Benzoyl
M-cresol
Aryl alkyl ketone
Phenylalkylamine
Aniline or substituted anilines
1-hydroxy-4-unsubstituted benzenoid
Secondary aliphatic/aromatic amine
Phenol
1-hydroxy-2-unsubstituted benzenoid
Toluene
Monocyclic benzene moiety
Cyclopentanol
Benzenoid
Tertiary alcohol
Alpha-hydroxy ketone
Vinylogous acid
1,3-aminoalcohol
Cyclic alcohol
Secondary alcohol
Carbonic acid derivative
Urea
Amino acid or derivatives
Carboxylic acid ester
1,2-aminoalcohol
Secondary amine
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organonitrogen compound
Organic oxide
Organopnictogen compound
Hydrocarbon derivative
Organic nitrogen compound
Alcohol
Amine
Primary aliphatic amine
Primary alcohol
Primary amine
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic 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	0.52	ALOGPS
logP	-0.21	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	9.86	ChemAxon
pKa (Strongest Basic)	7.63	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	214.91 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	149.4 m³·mol⁻¹	ChemAxon
Polarizability	58.86 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

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00017796

Chemspider ID

57261732

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

89787647

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Dobashi K, Isshiki K, Sawa T, Obata T, Hamada M, Naganawa H, Takita T, Takeuchi T, Umezawa H, Bei HS, et al.: 8''-Hydroxypactamycin and 7-deoxypactamycin, new members of the pactamycin group. J Antibiot (Tokyo). 1986 Dec;39(12):1779-83. doi: 10.7164/antibiotics.39.1779. [PubMed:3818452 ]

Showing NP-Card for 8''-Hydroxypactamycin (NP0061954)

MOL for NP0061954 (8''-Hydroxypactamycin)

3D MOL for NP0061954 (8''-Hydroxypactamycin)

3D SDF for NP0061954 (8''-Hydroxypactamycin)

3D-SDF for NP0061954 (8''-Hydroxypactamycin)

PDB for NP0061954 (8''-Hydroxypactamycin)

3D PDB for NP0061954 (8''-Hydroxypactamycin)

SMILES for NP0061954 (8''-Hydroxypactamycin)

INCHI for NP0061954 (8''-Hydroxypactamycin)

Structure for NP0061954 (8''-Hydroxypactamycin)

3D Structure for NP0061954 (8''-Hydroxypactamycin)