NP-MRD: Showing NP-Card for Holomycin (NP0023138)

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Record Information

Version

2.0

Created at

2021-01-06 08:15:21 UTC

Updated at

2021-07-15 17:40:56 UTC

NP-MRD ID

NP0023138

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Holomycin

Provided By

NPAtlas

Description

HOLOMYCIN is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Holomycin is found in Streptomyces, Streptomyces albidoflavus, Streptomyces clavuligerus, Streptomyces coelicolor, Streptomyces flavovirens, Streptomyces griseus, Streptomyces jumonjinensis and Streptomyces katsurahamanus. Holomycin was first documented in 1977 (PMID: 863793). Based on a literature review a small amount of articles have been published on HOLOMYCIN (PMID: 11158751) (PMID: 12426344) (PMID: 16890414).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242105393D          

 19 20  0  0  0  0            999 V2000
   -3.4786    0.7641   -0.5400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0974    0.2436   -0.6493 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7239   -0.2104   -1.7581 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2365    0.2668    0.4798 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0885   -0.2170    0.4285 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2475    0.5065    0.1026 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5975    2.1229   -0.3382 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.6488    1.8171   -0.5263 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.6136    0.1635   -0.1167 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3874   -0.3737    0.1721 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8418   -1.5860    0.5390 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5069   -1.4758    0.6831 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2115   -2.4745    1.0199 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1216   -0.0884   -0.2168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5689    1.5358    0.2568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8374    1.2177   -1.4893 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6380    0.6671    1.3692 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5703   -0.4263   -0.0949 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4114   -2.4531    0.6784 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  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  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12  5  1  0  0  0  0
 10  6  1  0  0  0  0
  1 14  1  0  0  0  0
  1 15  1  0  0  0  0
  1 16  1  0  0  0  0
  4 17  1  0  0  0  0
  9 18  1  0  0  0  0
 11 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0023138

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]N(C(=O)C([H])([H])[H])C1=C2SSC([H])=C2N([H])C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H6N2O2S2/c1-3(10)8-5-6-4(2-12-13-6)9-7(5)11/h2H,1H3,(H,8,10)(H,9,11)

> <INCHI_KEY>
HBUNPJGMNVQSBX-UHFFFAOYSA-N

> <FORMULA>
C7H6N2O2S2

> <MOLECULAR_WEIGHT>
214.26

> <EXACT_MASS>
213.987069789

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
19.798137831765477

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-{5-oxo-4H,5H-[1,2]dithiolo[4,3-b]pyrrol-6-yl}acetamide

> <ALOGPS_LOGP>
0.50

> <JCHEM_LOGP>
-0.7511626809999996

> <ALOGPS_LOGS>
-2.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.943282721677637

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.73655957985594

> <JCHEM_PKA_STRONGEST_BASIC>
-4.961512517358382

> <JCHEM_POLAR_SURFACE_AREA>
58.2

> <JCHEM_REFRACTIVITY>
55.44980000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.10e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
holomycin

> <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  C   UNK     0      -3.479   0.764  -0.540  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.097   0.244  -0.649  0.00  0.00           C+0
HETATM    3  O   UNK     0      -1.724  -0.210  -1.758  0.00  0.00           O+0
HETATM    4  N   UNK     0      -1.236   0.267   0.480  0.00  0.00           N+0
HETATM    5  C   UNK     0       0.089  -0.217   0.429  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.248   0.506   0.103  0.00  0.00           C+0
HETATM    7  S   UNK     0       1.597   2.123  -0.338  0.00  0.00           S+0
HETATM    8  S   UNK     0       3.649   1.817  -0.526  0.00  0.00           S+0
HETATM    9  C   UNK     0       3.614   0.164  -0.117  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.387  -0.374   0.172  0.00  0.00           C+0
HETATM   11  N   UNK     0       1.842  -1.586   0.539  0.00  0.00           N+0
HETATM   12  C   UNK     0       0.507  -1.476   0.683  0.00  0.00           C+0
HETATM   13  O   UNK     0      -0.212  -2.474   1.020  0.00  0.00           O+0
HETATM   14  H   UNK     0      -4.122  -0.088  -0.217  0.00  0.00           H+0
HETATM   15  H   UNK     0      -3.569   1.536   0.257  0.00  0.00           H+0
HETATM   16  H   UNK     0      -3.837   1.218  -1.489  0.00  0.00           H+0
HETATM   17  H   UNK     0      -1.638   0.667   1.369  0.00  0.00           H+0
HETATM   18  H   UNK     0       4.570  -0.426  -0.095  0.00  0.00           H+0
HETATM   19  H   UNK     0       2.411  -2.453   0.678  0.00  0.00           H+0
CONECT    1    2   14   15   16                                             
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   17                                                  
CONECT    5    4    6   12                                                  
CONECT    6    5    7   10                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   18                                                  
CONECT   10    9   11    6                                                  
CONECT   11   10   12   19                                                  
CONECT   12   11   13    5                                                  
CONECT   13   12                                                            
CONECT   14    1                                                            
CONECT   15    1                                                            
CONECT   16    1                                                            
CONECT   17    4                                                            
CONECT   18    9                                                            
CONECT   19   11                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
6-(Acetylamino)-1,2-dithiolo[4,3-b]pyrrol-5(4H)-one	ChEBI
6-Acetamido-1,2-dithiolo[4,3-b]pyrrol-5(4H)-one	ChEBI
N-(4,5-Dihydro-5-oxo-1,2-dithiolo-[4,3-b]pyrrol-6-yl)acetamide	ChEBI
N-(5-oxo-4H-Dithiolo[4,3-b]pyrrol-6-yl)acetamide	ChEBI
N-Demethylthiolutin	ChEBI
N-{5-oxo-4H,5H-[1,2]dithiolo[4,3-b]pyrrol-6-yl}acetamide	ChEBI

Chemical Formula

C₇H₆N₂O₂S₂

Average Mass

214.2600 Da

Monoisotopic Mass

213.98707 Da

IUPAC Name

N-{5-oxo-4H,5H-[1,2]dithiolo[4,3-b]pyrrol-6-yl}acetamide

Traditional Name

holomycin

CAS Registry Number

Not Available

SMILES

CC(=O)NC1=C2SSC=C2NC1=O

InChI Identifier

InChI=1S/C7H6N2O2S2/c1-3(10)8-5-6-4(2-12-13-6)9-7(5)11/h2H,1H3,(H,8,10)(H,9,11)

InChI Key

HBUNPJGMNVQSBX-UHFFFAOYSA-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	863793
Streptomyces albidoflavus	LOTUS Database	35616633
Streptomyces clavuligerus	LOTUS Database	35616633
Streptomyces coelicolor	LOTUS Database	35616633
Streptomyces flavovirens	LOTUS Database	35616633
Streptomyces griseus	LOTUS Database	35616633
Streptomyces jumonjinensis	LOTUS Database	35616633
Streptomyces katsurahamanus	LOTUS Database	35616633

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	0.5	ALOGPS
logP	-0.75	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	8.74	ChemAxon
pKa (Strongest Basic)	-5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	58.2 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	55.45 m³·mol⁻¹	ChemAxon
Polarizability	19.8 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

NPA013565

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

8438162

KEGG Compound ID

Not Available

BioCyc ID

CPD-17940

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10262683

PDB ID

Not Available

ChEBI ID

156451

Good Scents ID

Not Available

References

General References

Okamura K, Soga K, Shimauchi Y, Ishikura T, Lein J: Holomycin and N-propionylholothin, antibiotics produced by a cephamycin C producer. J Antibiot (Tokyo). 1977 Apr;30(4):334-6. doi: 10.7164/antibiotics.30.334. [PubMed:863793 ]
Oliva B, O'Neill A, Wilson JM, O'Hanlon PJ, Chopra I: Antimicrobial properties and mode of action of the pyrrothine holomycin. Antimicrob Agents Chemother. 2001 Feb;45(2):532-9. doi: 10.1128/AAC.45.2.532-539.2001. [PubMed:11158751 ]
de la Fuente A, Lorenzana LM, Martin JF, Liras P: Mutants of Streptomyces clavuligerus with disruptions in different genes for clavulanic acid biosynthesis produce large amounts of holomycin: possible cross-regulation of two unrelated secondary metabolic pathways. J Bacteriol. 2002 Dec;184(23):6559-65. doi: 10.1128/JB.184.23.6559-6565.2002. [PubMed:12426344 ]
Hou YH, Li FC, Wang SJ, Qin S, Wang QF: Intergeneric conjugation in holomycin-producing marine Streptomyces sp. strain M095. Microbiol Res. 2008;163(1):96-104. doi: 10.1016/j.micres.2006.07.003. Epub 2006 Aug 4. [PubMed:16890414 ]

Showing NP-Card for Holomycin (NP0023138)

MOL for NP0023138 (Holomycin)

3D MOL for NP0023138 (Holomycin)

3D SDF for NP0023138 (Holomycin)

3D-SDF for NP0023138 (Holomycin)

PDB for NP0023138 (Holomycin)

3D PDB for NP0023138 (Holomycin)

SMILES for NP0023138 (Holomycin)

INCHI for NP0023138 (Holomycin)

Structure for NP0023138 (Holomycin)

3D Structure for NP0023138 (Holomycin)