NP-MRD: Showing NP-Card for Hydantocidin (NP0009063)

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Record Information

Version

2.0

Created at

2020-12-09 06:31:39 UTC

Updated at

2021-07-15 17:02:12 UTC

NP-MRD ID

NP0009063

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Hydantocidin

Provided By

NPAtlas

Description

Hydantocidin belongs to the class of organic compounds known as hydantoins. These are heterocyclic compounds containing an imidazolidine substituted by ketone group at positions 2 and 4. Hydantocidin is found in Streptomyces and Streptomyces hygroscopicus. Hydantocidin was first documented in 1991 (PMID: 2026555). Based on a literature review a small amount of articles have been published on Hydantocidin (PMID: 33652162) (PMID: 31242546) (PMID: 31048991) (PMID: 29165398).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242106323D          

 25 26  0  0  0  0            999 V2000
   -3.6219   -2.2547    0.3536 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8075   -1.3310    0.0294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5631   -0.8080   -1.2841 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5752    0.2002   -1.1180 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4129    1.0913   -1.9933 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9218   -0.0647    0.1507 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9771   -0.6432    0.9562 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1057   -1.0084   -0.0885 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1628   -0.1715   -0.3924 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4714   -0.9032   -0.5392 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8051   -1.5576    0.6235 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1586    0.7581    0.8066 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9371    1.8676    0.6315 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3271    1.0740    0.8683 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5281    2.3189    0.3807 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0446   -1.1421   -2.1437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1423   -0.6000    1.9796 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9043    0.3743   -1.3106 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4060   -1.5358   -1.4287 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2485   -0.1200   -0.7391 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7897   -1.7537    0.6492 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4496    0.1555    1.6886 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4765    2.5118    0.0606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6233    1.0608    1.9519 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3703    2.4815   -0.0928 H   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  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  9 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
  7  2  1  0  0  0  0
 14  6  1  0  0  0  0
  3 16  1  0  0  0  0
  7 17  1  0  0  0  0
  9 18  1  6  0  0  0
 10 19  1  0  0  0  0
 10 20  1  0  0  0  0
 11 21  1  0  0  0  0
 12 22  1  1  0  0  0
 13 23  1  0  0  0  0
 14 24  1  1  0  0  0
 15 25  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0009063

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@@]1([H])O[C@@]2(N([H])C(=O)N([H])C2=O)[C@]([H])(O[H])[C@]1([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C7H10N2O6/c10-1-2-3(11)4(12)7(15-2)5(13)8-6(14)9-7/h2-4,10-12H,1H2,(H2,8,9,13,14)/t2-,3-,4-,7+/m1/s1

> <INCHI_KEY>
RFZZKBWDDKMWNM-GTBMBKLPSA-N

> <FORMULA>
C7H10N2O6

> <MOLECULAR_WEIGHT>
218.165

> <EXACT_MASS>
218.05388605

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
18.607432880531665

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(5S,7R,8S,9R)-8,9-dihydroxy-7-(hydroxymethyl)-6-oxa-1,3-diazaspiro[4.4]nonane-2,4-dione

> <ALOGPS_LOGP>
-2.11

> <JCHEM_LOGP>
-2.6951622696666666

> <ALOGPS_LOGS>
0.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.559189502071819

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.213377073822999

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9809290565714806

> <JCHEM_POLAR_SURFACE_AREA>
128.12

> <JCHEM_REFRACTIVITY>
43.003499999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.65e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(5S,7R,8S,9R)-8,9-dihydroxy-7-(hydroxymethyl)-6-oxa-1,3-diazaspiro[4.4]nonane-2,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  O   UNK     0      -3.622  -2.255   0.354  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.808  -1.331   0.029  0.00  0.00           C+0
HETATM    3  N   UNK     0      -2.563  -0.808  -1.284  0.00  0.00           N+0
HETATM    4  C   UNK     0      -1.575   0.200  -1.118  0.00  0.00           C+0
HETATM    5  O   UNK     0      -1.413   1.091  -1.993  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.922  -0.065   0.151  0.00  0.00           C+0
HETATM    7  N   UNK     0      -1.977  -0.643   0.956  0.00  0.00           N+0
HETATM    8  O   UNK     0       0.106  -1.008  -0.089  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.163  -0.172  -0.392  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.471  -0.903  -0.539  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.805  -1.558   0.624  0.00  0.00           O+0
HETATM   12  C   UNK     0       1.159   0.758   0.807  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.937   1.868   0.632  0.00  0.00           O+0
HETATM   14  C   UNK     0      -0.327   1.074   0.868  0.00  0.00           C+0
HETATM   15  O   UNK     0      -0.528   2.319   0.381  0.00  0.00           O+0
HETATM   16  H   UNK     0      -3.045  -1.142  -2.144  0.00  0.00           H+0
HETATM   17  H   UNK     0      -2.142  -0.600   1.980  0.00  0.00           H+0
HETATM   18  H   UNK     0       0.904   0.374  -1.311  0.00  0.00           H+0
HETATM   19  H   UNK     0       2.406  -1.536  -1.429  0.00  0.00           H+0
HETATM   20  H   UNK     0       3.248  -0.120  -0.739  0.00  0.00           H+0
HETATM   21  H   UNK     0       3.790  -1.754   0.649  0.00  0.00           H+0
HETATM   22  H   UNK     0       1.450   0.156   1.689  0.00  0.00           H+0
HETATM   23  H   UNK     0       1.476   2.512   0.061  0.00  0.00           H+0
HETATM   24  H   UNK     0      -0.623   1.061   1.952  0.00  0.00           H+0
HETATM   25  H   UNK     0      -1.370   2.482  -0.093  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4   16                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8   14                                             
CONECT    7    6    2   17                                                  
CONECT    8    6    9                                                       
CONECT    9    8   10   12   18                                             
CONECT   10    9   11   19   20                                             
CONECT   11   10   21                                                       
CONECT   12    9   13   14   22                                             
CONECT   13   12   23                                                       
CONECT   14   12   15    6   24                                             
CONECT   15   14   25                                                       
CONECT   16    3                                                            
CONECT   17    7                                                            
CONECT   18    9                                                            
CONECT   19   10                                                            
CONECT   20   10                                                            
CONECT   21   11                                                            
CONECT   22   12                                                            
CONECT   23   13                                                            
CONECT   24   14                                                            
CONECT   25   15                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   52    0
END

View in JSmol View NMR Assignments

Synonyms

Not Available

Chemical Formula

C₇H₁₀N₂O₆

Average Mass

218.1650 Da

Monoisotopic Mass

218.05389 Da

IUPAC Name

(5S,7R,8S,9R)-8,9-dihydroxy-7-(hydroxymethyl)-6-oxa-1,3-diazaspiro[4.4]nonane-2,4-dione

Traditional Name

(5S,7R,8S,9R)-8,9-dihydroxy-7-(hydroxymethyl)-6-oxa-1,3-diazaspiro[4.4]nonane-2,4-dione

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@]2(NC(=O)NC2=O)[C@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C7H10N2O6/c10-1-2-3(11)4(12)7(15-2)5(13)8-6(14)9-7/h2-4,10-12H,1H2,(H2,8,9,13,14)/t2-,3-,4-,7+/m1/s1

InChI Key

RFZZKBWDDKMWNM-GTBMBKLPSA-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	NPAtlas	2026555
Streptomyces hygroscopicus	LOTUS Database	35616633

Species Where Detected

Species Name	Source	Reference
Streptomyces hygroscopicus SANK 63584	KNApSAcK Database	22123792

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydantoins. These are heterocyclic compounds containing an imidazolidine substituted by ketone group at positions 2 and 4.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Azolidines

Sub Class

Imidazolidines

Direct Parent

Hydantoins

Alternative Parents

Substituents

Hydantoin
Alpha-amino acid or derivatives
5-monosubstituted hydantoin
N-acyl urea
Ureide
Monosaccharide
Dicarboximide
Tetrahydrofuran
Carbonic acid derivative
Secondary alcohol
Urea
Carboxylic acid derivative
Oxacycle
Azacycle
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Carbonyl group
Organooxygen compound
Primary alcohol
Organic nitrogen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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	-2.1	ALOGPS
logP	-2.7	ChemAxon
logS	0.08	ALOGPS
pKa (Strongest Acidic)	8.21	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	128.12 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	43 m³·mol⁻¹	ChemAxon
Polarizability	18.61 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA020674

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00017079

Chemspider ID

111605

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

125429

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Nakajima M, Itoi K, Takamatsu Y, Kinoshita T, Okazaki T, Kawakubo K, Shindo M, Honma T, Tohjigamori M, Haneishi T: Hydantocidin: a new compound with herbicidal activity from Streptomyces hygroscopicus. J Antibiot (Tokyo). 1991 Mar;44(3):293-300. doi: 10.7164/antibiotics.44.293. [PubMed:2026555 ]
Chidambaram S, Mostafa AA, Abdulrahman Al-Askar A, Sayed SRM, Radhakrishnan S, Akbar I: Green catalyst Cu(II)-enzyme-mediated eco-friendly synthesis of 2-pyrimidinamines as potential larvicides against Culex quinquefasciatus mosquito and toxicity investigation against non-target aquatic species. Bioorg Chem. 2021 Apr;109:104697. doi: 10.1016/j.bioorg.2021.104697. Epub 2021 Feb 8. [PubMed:33652162 ]
Stathi A, Mamais M, Chrysina ED, Gimisis T: Anomeric Spironucleosides of beta-d-Glucopyranosyl Uracil as Potential Inhibitors of Glycogen Phosphorylase. Molecules. 2019 Jun 25;24(12). pii: molecules24122327. doi: 10.3390/molecules24122327. [PubMed:31242546 ]
Arif IA, Ahamed A, Kumar RS, Idhayadhulla A, Manilal A: Cytotoxic, larvicidal, nematicidal, and antifeedant activities of piperidin-connected 2-thioxoimidazolidin-4-one derivatives. Saudi J Biol Sci. 2019 May;26(4):673-680. doi: 10.1016/j.sjbs.2017.12.007. Epub 2017 Dec 24. [PubMed:31048991 ]
Soengas RG, da Silva G, Estevez JC: Synthesis of Spironucleosides: Past and Future Perspectives. Molecules. 2017 Nov 22;22(11). pii: molecules22112028. doi: 10.3390/molecules22112028. [PubMed:29165398 ]

Showing NP-Card for Hydantocidin (NP0009063)

MOL for NP0009063 (Hydantocidin)

3D MOL for NP0009063 (Hydantocidin)

3D SDF for NP0009063 (Hydantocidin)

3D-SDF for NP0009063 (Hydantocidin)

PDB for NP0009063 (Hydantocidin)

3D PDB for NP0009063 (Hydantocidin)

SMILES for NP0009063 (Hydantocidin)

INCHI for NP0009063 (Hydantocidin)

Structure for NP0009063 (Hydantocidin)

3D Structure for NP0009063 (Hydantocidin)