Natural Product: ENC003196

NPs Basic Information

Download MOL File
Name
Palmarumycin B3
Molecular Formula C20H18O8
IUPAC Name*
(1S,2S,3S,4R,6S,7R,10S)-spiro[11-oxatricyclo[4.4.1.01,6]undec-8-ene-5,3'-2,4-dioxatricyclo[7.3.1.05,13]trideca-1(12),5,7,9(13),10-pentaene]-2,3,4,7,10-pentol
SMILES
C1=CC2=C3C(=C1)OC4([C@@H]([C@H]([C@@H]([C@@]56[C@@]4(O5)[C@@H](C=C[C@@H]6O)O)O)O)O)OC3=CC=C2
InChI
InChI=1S/C20H18O8/c21-12-7-8-13(22)19-18(12,28-19)16(24)15(23)17(25)20(19)26-10-5-1-3-9-4-2-6-11(27-20)14(9)10/h1-8,12-13,15-17,21-25H/t12-,13+,15-,16-,17+,18-,19-/m0/s1
InChIKey
PKEIHANGEAWICI-XJOGIRLRSA-N
Synonyms
Palmarumycin B3; CHEMBL3342634
CAS NA
PubChem CID 101888371
ChEMBL ID CHEMBL3342634
*Note: the IUPAC Name was collected from PubChem.
Chemical Classification:
  • Kingdom: Organic compounds
    • Superclass: Benzenoids
      • Class: Naphthalenes
        • Subclass: No Rank at Level Subclass
          • Direct Parent: Naphthalenes

ClassyFire Version 1.0
PMID:27867422

NPs Species Source

Endophyte ID Endophyte Name Family Genus Taxonomy ID GenBank ID Closest GenBank ID Reference
Endophyte ID Endophyte Name Family Genus Taxonomy ID GenBank ID Closest GenBank ID Reference

NPs Content

*Note: The vaules in Content Percentage are calculated by dividing the content value by the maximum content value in NP Content.
**Note: The units with different NP content, due to their incomparable values, are separated into different tables.

NPs Biological Activity

Bioactivity Name Target ID Target Name Target Type Target Organism Target Organism ID Potency of Bioactivity Activity Type Value Unit Endophyte ID Endophyte Name
Bioactivity Name Target ID Target Name Target Type Target Organism Target Organism ID Potency of Bioactivity Activity Type Value Unit Endophyte ID Endophyte Name

NPs Physi-Chem Properties

Molecular Weight: 386.4 ALogp: -0.9
HBD: 5 HBA: 8
Rotatable Bonds: 0 Lipinski's rule of five: Accepted
Polar Surface Area: 132.0 Aromatic Rings: 6
Heavy Atoms: 28 QED Weighted: 0.307

NPs ADMET Properties*

ADMET: Absorption

Caco-2 Permeability: -5.753 MDCK Permeability: 0.00002870
Pgp-inhibitor: 0.003 Pgp-substrate: 0.21
Human Intestinal Absorption (HIA): 0.037 20% Bioavailability (F20%): 0.029
30% Bioavailability (F30%): 0.973

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB): 0.309 Plasma Protein Binding (PPB): 93.56%
Volume Distribution (VD): 0.48 Fu: 3.59%

ADMET: Metabolism

CYP1A2-inhibitor: 0.055 CYP1A2-substrate: 0.107
CYP2C19-inhibitor: 0.023 CYP2C19-substrate: 0.302
CYP2C9-inhibitor: 0.01 CYP2C9-substrate: 0.337
CYP2D6-inhibitor: 0.007 CYP2D6-substrate: 0.222
CYP3A4-inhibitor: 0.017 CYP3A4-substrate: 0.074

ADMET: Excretion

Clearance (CL): 5.477 Half-life (T1/2): 0.524

ADMET: Toxicity

hERG Blockers: 0.018 Human Hepatotoxicity (H-HT): 0.988
Drug-inuced Liver Injury (DILI): 0.933 AMES Toxicity: 0.587
Rat Oral Acute Toxicity: 0.592 Maximum Recommended Daily Dose: 0.026
Skin Sensitization: 0.139 Carcinogencity: 0.94
Eye Corrosion: 0.003 Eye Irritation: 0.013
Respiratory Toxicity: 0.978
*Note: the ADMET properties was calculated by ADMETlab 2.0. Reference: PMID: 33893803.

Similar Compounds*

Compounds similar to EMNPD with top10 similarity:

Similar NPs Similar Drugs
NPs ID NPs 2D Structure Similarity Score TTD ID Drug 2D Structure Similarity Score
ENC002185 0.784 D0Q3VE 0.264
ENC003197 0.736 D06BQU 0.229
ENC003194 0.717 D01TNW 0.227
ENC003195 0.629 D08DFX 0.221
ENC001988 0.570 D08CCE 0.219
ENC001999 0.570 D06ALD 0.219
ENC003239 0.544 D0AZ8C 0.212
ENC002330 0.544 D06TJJ 0.208
ENC003198 0.524 D00JRA 0.202
ENC003238 0.500 D0O6IZ 0.198
*Note: the compound similarity was calculated by RDKIT.