Structure

Physi-Chem Properties

Molecular Weight:  260.1
Volume:  258.385
LogP:  2.828
LogD:  3.002
LogS:  -4.448
# Rotatable Bonds:  0
TPSA:  51.97
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.409
Synthetic Accessibility Score:  5.798
Fsp3:  0.533
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:  -4.714
MDCK Permeability:  2.515300911909435e-05
Pgp-inhibitor:  0.014
Pgp-substrate:  0.019
Human Intestinal Absorption (HIA):  0.014
20% Bioavailability (F20%):  0.016
30% Bioavailability (F30%):  0.015

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.408
Plasma Protein Binding (PPB):  91.41471099853516%
Volume Distribution (VD):  1.593
Pgp-substrate:  5.216315269470215%

ADMET: Metabolism

CYP1A2-inhibitor:  0.053
CYP1A2-substrate:  0.641
CYP2C19-inhibitor:  0.651
CYP2C19-substrate:  0.668
CYP2C9-inhibitor:  0.181
CYP2C9-substrate:  0.08
CYP2D6-inhibitor:  0.027
CYP2D6-substrate:  0.781
CYP3A4-inhibitor:  0.659
CYP3A4-substrate:  0.362

ADMET: Excretion

Clearance (CL):  12.864
Half-life (T1/2):  0.261

ADMET: Toxicity

hERG Blockers:  0.014
Human Hepatotoxicity (H-HT):  0.553
Drug-inuced Liver Injury (DILI):  0.863
AMES Toxicity:  0.787
Rat Oral Acute Toxicity:  0.924
Maximum Recommended Daily Dose:  0.077
Skin Sensitization:  0.497
Carcinogencity:  0.657
Eye Corrosion:  0.029
Eye Irritation:  0.102
Respiratory Toxicity:  0.966

Download Data

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

  Natural Product: NPC73347

Natural Product ID:  NPC73347
Common Name*:   KBMSVODXFLAQNJ-IUKAEILTSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  KBMSVODXFLAQNJ-IUKAEILTSA-N
Standard InCHI:  InChI=1S/C15H16O4/c1-8-4-3-5-15-13(19-15)12(18-14(15)16)11-9(2)7-17-10(11)6-8/h4,7,12-13H,3,5-6H2,1-2H3/b8-4+/t12-,13-,15?/m0/s1
SMILES:  C/C/1=CCCC23[C@H]([C@H](c4c(C)coc4C1)OC2=O)O3
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   6450227
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000368] Dioxanes
        • [CHEMONTID:0001313] 1,4-dioxanes

*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
NPO15351 Streptomyces prunicolor Species Streptomycetaceae Bacteria n.a. mycelium n.a. DOI[10.1021/np50098a008]
NPO6541 Scrophularia buergeriana Species Scrophulariaceae Eukaryota roots n.a. n.a. PMID[12444706]
NPO11898 Lobophora variegata Species Dictyotaceae Eukaryota n.a. at depths of 630 m at El Mdano (Tenerife, Canary Islands) n.a. PMID[26126835]
NPO5247 Elaphoglossum lindbergii Species Dryopteridaceae Eukaryota n.a. n.a. n.a. PMID[26689830]
NPO6541 Scrophularia buergeriana Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12853 Leucocarpus perfoliatus Species Phrymaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12633 Rapanea neurophylla Species Primulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10530 Aconitum subcuneatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12633 Rapanea neurophylla Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6541 Scrophularia buergeriana Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11206 Trifolium hybridum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10530 Aconitum subcuneatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12853 Leucocarpus perfoliatus Species Phrymaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10530 Aconitum subcuneatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6541 Scrophularia buergeriana Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6541 Scrophularia buergeriana Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1044 Caiman crocodilus Species Alligatoridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10530 Aconitum subcuneatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11898 Lobophora variegata Species Dictyotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1116 Periconia atropurpurea Species Periconiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5714 Rogeria adenophylla Species Pedaliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11527 Ibacus peronii Species Scyllaridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5247 Elaphoglossum lindbergii Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15351 Streptomyces prunicolor Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12633 Rapanea neurophylla Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2996 Pistacia atlantica Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9363 Ferula ammoniacum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7560 Tachardia acaciae n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO6541 Scrophularia buergeriana Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9606 Castanea dentata Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2207 Sphaerella rubella n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO11206 Trifolium hybridum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12146 Stemodia maritima Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23883 Penicillium abidjanum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12853 Leucocarpus perfoliatus Species Phrymaceae 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

☑ 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 NPC73347 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

  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 NPC73347 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

  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