NP-MRD: Showing NP-Card for Pyramidamycin C (NP0011163)

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Record Information

Version

1.0

Created at

2021-01-05 20:57:02 UTC

Updated at

2021-07-15 17:08:08 UTC

NP-MRD ID

NP0011163

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pyramidamycin C

Provided By

NPAtlas

Description

Pyramidamycin C is found in Streptomyces sp. DGC1. It was first documented in 2012 (PMID: 23047245). Based on a literature review a significant number of articles have been published on 3-amino-2-hydroxy-4-methoxybenzene-1-carboximidic acid (PMID: 34607389) (PMID: 34607359) (PMID: 34607322) (PMID: 34607314) (PMID: 34607263) (PMID: 34607258).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242107443D          

 23 23  0  0  0  0            999 V2000
   -3.4903   -1.1733    0.6795 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6245   -0.2657    0.0652 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2509   -0.2827    0.1474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6133   -1.2555    0.8853 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7619   -1.2298    0.9365 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4977   -0.2570    0.2684 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9530   -0.2792    0.3585 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6657    0.7320   -0.3388 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4959   -1.1808    1.0399 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8314    0.7129   -0.4689 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6086    1.6535   -1.1116 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5400    0.6845   -0.5180 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2159    1.7021   -1.2903 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5107   -0.7092    0.7761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1506   -1.5175    1.6585 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6565   -2.0708    0.0176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1878   -2.0118    1.4046 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2393   -2.0058    1.5235 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0364    1.5791    0.1552 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8339    0.6427   -1.3790 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2321    2.4082   -1.6781 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9068    2.6851   -1.2360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0087    1.4387   -1.8955 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
  6 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
 12 13  1  0  0  0  0
 12  3  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
  5 18  1  0  0  0  0
  8 19  1  0  0  0  0
  8 20  1  0  0  0  0
 11 21  1  0  0  0  0
 13 22  1  0  0  0  0
 13 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0011163

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C(N([H])[H])C(OC([H])([H])[H])=C([H])C([H])=C1C(=O)N([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C8H10N2O3/c1-13-5-3-2-4(8(10)12)7(11)6(5)9/h2-3,11H,9H2,1H3,(H2,10,12)

> <INCHI_KEY>
ADSMKVUNHDDYBH-UHFFFAOYSA-N

> <FORMULA>
C8H10N2O3

> <MOLECULAR_WEIGHT>
182.179

> <EXACT_MASS>
182.06914219

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
17.93809516438058

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-amino-2-hydroxy-4-methoxybenzamide

> <ALOGPS_LOGP>
0.08

> <JCHEM_LOGP>
0.1837235690000004

> <ALOGPS_LOGS>
-1.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.616342587786342

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.00480220876072

> <JCHEM_PKA_STRONGEST_BASIC>
3.596010048800498

> <JCHEM_POLAR_SURFACE_AREA>
98.57

> <JCHEM_REFRACTIVITY>
48.28090000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.26e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-amino-2-hydroxy-4-methoxybenzamide

> <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      -3.490  -1.173   0.680  0.00  0.00           C+0
HETATM    2  O   UNK     0      -2.624  -0.266   0.065  0.00  0.00           O+0
HETATM    3  C   UNK     0      -1.251  -0.283   0.147  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.613  -1.256   0.885  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.762  -1.230   0.937  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.498  -0.257   0.268  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.953  -0.279   0.359  0.00  0.00           C+0
HETATM    8  N   UNK     0       3.666   0.732  -0.339  0.00  0.00           N+0
HETATM    9  O   UNK     0       3.496  -1.181   1.040  0.00  0.00           O+0
HETATM   10  C   UNK     0       0.831   0.713  -0.469  0.00  0.00           C+0
HETATM   11  O   UNK     0       1.609   1.654  -1.112  0.00  0.00           O+0
HETATM   12  C   UNK     0      -0.540   0.685  -0.518  0.00  0.00           C+0
HETATM   13  N   UNK     0      -1.216   1.702  -1.290  0.00  0.00           N+0
HETATM   14  H   UNK     0      -4.511  -0.709   0.776  0.00  0.00           H+0
HETATM   15  H   UNK     0      -3.151  -1.518   1.659  0.00  0.00           H+0
HETATM   16  H   UNK     0      -3.656  -2.071   0.018  0.00  0.00           H+0
HETATM   17  H   UNK     0      -1.188  -2.012   1.405  0.00  0.00           H+0
HETATM   18  H   UNK     0       1.239  -2.006   1.524  0.00  0.00           H+0
HETATM   19  H   UNK     0       4.036   1.579   0.155  0.00  0.00           H+0
HETATM   20  H   UNK     0       3.834   0.643  -1.379  0.00  0.00           H+0
HETATM   21  H   UNK     0       1.232   2.408  -1.678  0.00  0.00           H+0
HETATM   22  H   UNK     0      -0.907   2.685  -1.236  0.00  0.00           H+0
HETATM   23  H   UNK     0      -2.009   1.439  -1.896  0.00  0.00           H+0
CONECT    1    2   14   15   16                                             
CONECT    2    1    3                                                       
CONECT    3    2    4   12                                                  
CONECT    4    3    5   17                                                  
CONECT    5    4    6   18                                                  
CONECT    6    5    7   10                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7   19   20                                                  
CONECT    9    7                                                            
CONECT   10    6   11   12                                                  
CONECT   11   10   21                                                       
CONECT   12   10   13    3                                                  
CONECT   13   12   22   23                                                  
CONECT   14    1                                                            
CONECT   15    1                                                            
CONECT   16    1                                                            
CONECT   17    4                                                            
CONECT   18    5                                                            
CONECT   19    8                                                            
CONECT   20    8                                                            
CONECT   21   11                                                            
CONECT   22   13                                                            
CONECT   23   13                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   46    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
3-Amino-2-hydroxy-4-methoxybenzene-1-carboximidate	Generator

Chemical Formula

C₈H₁₀N₂O₃

Average Mass

182.1790 Da

Monoisotopic Mass

182.06914 Da

IUPAC Name

3-amino-2-hydroxy-4-methoxybenzamide

Traditional Name

3-amino-2-hydroxy-4-methoxybenzamide

CAS Registry Number

Not Available

SMILES

COC1=C(N)C(O)=C(C=C1)C(N)=O

InChI Identifier

InChI=1S/C8H10N2O3/c1-13-5-3-2-4(8(10)12)7(11)6(5)9/h2-3,11H,9H2,1H3,(H2,10,12)

InChI Key

ADSMKVUNHDDYBH-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 sp. DGC1	NPAtlas	23047245

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	0.08	ALOGPS
logP	0.18	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	9	ChemAxon
pKa (Strongest Basic)	3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	98.57 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	48.28 m³·mol⁻¹	ChemAxon
Polarizability	17.94 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA017794

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

29215411

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

71482612

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Shaaban KA, Shepherd MD, Ahmed TA, Nybo SE, Leggas M, Rohr J: Pyramidamycins A-D and 3-hydroxyquinoline-2-carboxamide; cytotoxic benzamides from Streptomyces sp. DGC1. J Antibiot (Tokyo). 2012 Dec;65(12):615-22. doi: 10.1038/ja.2012.81. Epub 2012 Oct 10. [PubMed:23047245 ]
Shan M, Meng F, Zhou L, Lu F, Bie X, Zhao H, Lu Z: Surfactin inhibits the growth of Propionibacterium acnes by destroying the cell wall and membrane. Lett Appl Microbiol. 2021 Oct 4. doi: 10.1111/lam.13576. [PubMed:34607389 ]
Reddy CA, Wenzke K, Watts LS, Armstrong M, Chen VL, Baker JR, Chen JW: Phenotyping patients with borderline elevated esophageal acid exposure. Dis Esophagus. 2021 Oct 5. pii: 6381246. doi: 10.1093/dote/doab071. [PubMed:34607359 ]
Wei L, Boutouil H, Gerbatin RR, Mamad O, Heiland M, Reschke CR, Del Gallo F, Fabene PF, Henshall DC, Lowery M, Morris G, Mooney C: Detection of spontaneous seizures in EEGs in multiple experimental mouse models of epilepsy. J Neural Eng. 2021 Oct 4. doi: 10.1088/1741-2552/ac2ca0. [PubMed:34607322 ]
An JN, Kim H, Kim EN, Cho A, Cho Y, Choi YW, Kim JH, Yang SH, Choi BS, Lim CS, Kim YS, Kim KP, Lee JP: Effects of periostin deficiency on kidney aging and lipid metabolism. Aging (Albany NY). 2021 Oct 3;13(undefined). pii: 203580. doi: 10.18632/aging.203580. [PubMed:34607314 ]
He Z, Li Y, Liu C, Li Y, Qian M, Zhu Y, Wang X: Controllable conversion of biomass to lignin-silica hybrid nanoparticles: High-performance renewable dual-phase fillers. Waste Manag. 2021 Oct 1;135:381-388. doi: 10.1016/j.wasman.2021.09.025. [PubMed:34607263 ]
Larrouture QC, Tourkova IL, Stolz DB, Riazanski V, Onwuka KM, Franks JM, Dobrowolski SF, Nelson DJ, Schlesinger PH, Blair HC: Growth and mineralization of osteoblasts from mesenchymal stem cells on microporous membranes: Epithelial-like growth with transmembrane resistance and pH gradient. Biochem Biophys Res Commun. 2021 Sep 29;580:14-19. doi: 10.1016/j.bbrc.2021.09.075. [PubMed:34607258 ]
Shi Y, Wei Q, Liu Y, Yuan J: The alleviating effect of sphingosine kinases 2 inhibitor K145 on nonalcoholic fatty liver. Biochem Biophys Res Commun. 2021 Sep 28;580:1-6. doi: 10.1016/j.bbrc.2021.09.060. [PubMed:34607257 ]
Tang Y, Wang Q, Liu J: Microbiota-gut-brain axis: A novel potential target of ketogenic diet for epilepsy. Curr Opin Pharmacol. 2021 Oct 1;61:36-41. doi: 10.1016/j.coph.2021.08.018. [PubMed:34607252 ]

Showing NP-Card for Pyramidamycin C (NP0011163)

MOL for NP0011163 (Pyramidamycin C)

3D MOL for NP0011163 (Pyramidamycin C)

3D SDF for NP0011163 (Pyramidamycin C)

3D-SDF for NP0011163 (Pyramidamycin C)

PDB for NP0011163 (Pyramidamycin C)

3D PDB for NP0011163 (Pyramidamycin C)

SMILES for NP0011163 (Pyramidamycin C)

INCHI for NP0011163 (Pyramidamycin C)

Structure for NP0011163 (Pyramidamycin C)

3D Structure for NP0011163 (Pyramidamycin C)