Structure

Physi-Chem Properties

Molecular Weight:  270.15
Volume:  272.266
LogP:  0.86
LogD:  0.324
LogS:  -1.933
# Rotatable Bonds:  4
TPSA:  61.83
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.772
Synthetic Accessibility Score:  4.677
Fsp3:  0.857
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.63
MDCK Permeability:  1.4051778634893708e-05
Pgp-inhibitor:  0.54
Pgp-substrate:  0.192
Human Intestinal Absorption (HIA):  0.013
20% Bioavailability (F20%):  0.017
30% Bioavailability (F30%):  0.035

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.539
Plasma Protein Binding (PPB):  52.164878845214844%
Volume Distribution (VD):  0.827
Pgp-substrate:  50.2497444152832%

ADMET: Metabolism

CYP1A2-inhibitor:  0.013
CYP1A2-substrate:  0.931
CYP2C19-inhibitor:  0.015
CYP2C19-substrate:  0.902
CYP2C9-inhibitor:  0.008
CYP2C9-substrate:  0.049
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.225
CYP3A4-inhibitor:  0.02
CYP3A4-substrate:  0.496

ADMET: Excretion

Clearance (CL):  11.616
Half-life (T1/2):  0.9

ADMET: Toxicity

hERG Blockers:  0.13
Human Hepatotoxicity (H-HT):  0.434
Drug-inuced Liver Injury (DILI):  0.839
AMES Toxicity:  0.063
Rat Oral Acute Toxicity:  0.163
Maximum Recommended Daily Dose:  0.023
Skin Sensitization:  0.544
Carcinogencity:  0.132
Eye Corrosion:  0.961
Eye Irritation:  0.819
Respiratory Toxicity:  0.207

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC233143

Natural Product ID:  NPC233143
Common Name*:   (-)-Botryodiplodin Dimer
IUPAC Name:   1-[(3S,4R,5S)-5-[(2S,3R,4S)-4-acetyl-3-methyloxolan-2-yl]oxy-4-methyloxolan-3-yl]ethanone
Synonyms:  
Standard InCHIKey:  LOKALHOVFCLNSO-IZIREBJPSA-N
Standard InCHI:  InChI=1S/C14H22O5/c1-7-11(9(3)15)5-17-13(7)19-14-8(2)12(6-18-14)10(4)16/h7-8,11-14H,5-6H2,1-4H3/t7-,8-,11-,12-,13+,14+/m1/s1
SMILES:  C[C@H]1[C@@H](OC[C@H]1C(=O)C)O[C@@H]1OC[C@H]([C@H]1C)C(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2251621
PubChem CID:   23583009
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001967] Oxolanes

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO15176 Centaurea deflexa Species Asteraceae Eukaryota aerial parts n.a. n.a. PMID[21458113]
NPO7413 Wedelia biflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15678 Scarites subterraneus Species Carabidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16622 Cathartus quadricollis Species Silvanidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15176 Centaurea deflexa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT2212 Organism Oncopeltus fasciatus Oncopeltus fasciatus LD50 > 15.0 ug PMID[571588]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC233143 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.8519 High Similarity NPC216382
0.7966 Intermediate Similarity NPC220894
0.6053 Remote Similarity NPC474754
0.6029 Remote Similarity NPC295256
0.5972 Remote Similarity NPC470243
0.5965 Remote Similarity NPC282440
0.5875 Remote Similarity NPC101138
0.5875 Remote Similarity NPC82492
0.5875 Remote Similarity NPC51135
0.5875 Remote Similarity NPC25802
0.5833 Remote Similarity NPC305182
0.5783 Remote Similarity NPC221993
0.5775 Remote Similarity NPC119838
0.5735 Remote Similarity NPC268243
0.5733 Remote Similarity NPC179922
0.5714 Remote Similarity NPC325102
0.5714 Remote Similarity NPC473899
0.569 Remote Similarity NPC308301
0.5676 Remote Similarity NPC474755
0.566 Remote Similarity NPC14608
0.5652 Remote Similarity NPC314103
0.561 Remote Similarity NPC478111
0.5606 Remote Similarity NPC132998
0.5606 Remote Similarity NPC322855
0.56 Remote Similarity NPC228727

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC233143 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.6029 Remote Similarity NPD9496 Clinical (unspecified phase)
0.5775 Remote Similarity NPD229 Approved

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data