Structure

Physi-Chem Properties

Molecular Weight:  1062.52
Volume:  1010.546
LogP:  0.177
LogD:  -0.175
LogS:  -2.928
# Rotatable Bonds:  14
TPSA:  363.13
# H-Bond Aceptor:  23
# H-Bond Donor:  13
# Rings:  9
# Heavy Atoms:  23

MedChem Properties

QED Drug-Likeness Score:  0.078
Synthetic Accessibility Score:  7.504
Fsp3:  0.941
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.418
MDCK Permeability:  6.186278915265575e-05
Pgp-inhibitor:  0.014
Pgp-substrate:  0.988
Human Intestinal Absorption (HIA):  0.999
20% Bioavailability (F20%):  0.962
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.3
Plasma Protein Binding (PPB):  52.011322021484375%
Volume Distribution (VD):  -0.012
Pgp-substrate:  13.277013778686523%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.98
CYP2C19-inhibitor:  0.0
CYP2C19-substrate:  0.21
CYP2C9-inhibitor:  0.0
CYP2C9-substrate:  0.001
CYP2D6-inhibitor:  0.0
CYP2D6-substrate:  0.014
CYP3A4-inhibitor:  0.091
CYP3A4-substrate:  0.04

ADMET: Excretion

Clearance (CL):  0.379
Half-life (T1/2):  0.88

ADMET: Toxicity

hERG Blockers:  0.349
Human Hepatotoxicity (H-HT):  0.2
Drug-inuced Liver Injury (DILI):  0.011
AMES Toxicity:  0.066
Rat Oral Acute Toxicity:  0.041
Maximum Recommended Daily Dose:  0.084
Skin Sensitization:  0.122
Carcinogencity:  0.568
Eye Corrosion:  0.003
Eye Irritation:  0.005
Respiratory Toxicity:  0.973

Download Data

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

  Natural Product: NPC208867

Natural Product ID:  NPC208867
Common Name*:   IQVWMDXKYQHJMP-VIFPVBQESA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  IQVWMDXKYQHJMP-VIFPVBQESA-N
Standard InCHI:  InChI=1S/C15H16O/c1-9-5-4-6-12-7-13-15(10(2)8-16-13)11(3)14(9)12/h4,6-9H,5H2,1-3H3/t9-/m0/s1
SMILES:  C[C@H]1CC=Cc2cc3c(c(C)co3)c(C)c12
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   638210
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0003655] Eremophilane, 8,9-secoeremophilane and furoeremophilane sesquiterpenoids

*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
NPO29103 Spongia matamata Species Spongiidae Eukaryota n.a. n.a. n.a. PMID[10075761]
NPO28939 Piptanthus nepalensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28939 Piptanthus nepalensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28939 Piptanthus nepalensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28829 Pelvetia wrightii Species Fucaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28974 Smilax ornata Species Staphylinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29103 Spongia matamata Species Spongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26540 Echinopsis spachiana Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29402 Launaea arborescens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29194 Harziella entomophila n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO29013 Annulohypoxylon cohaerens Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25969 Aspergillus nomius Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28870 Clausena lenis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11524 Macrotomia ugamensis Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28808 Piptanthus mongolicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28939 Piptanthus nepalensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29157 Reichardia gaditana 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

☑ 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 NPC208867 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 NPC208867 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