Structure

Physi-Chem Properties

Molecular Weight:  288.21
Volume:  315.262
LogP:  4.466
LogD:  3.611
LogS:  -4.682
# Rotatable Bonds:  1
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.713
Synthetic Accessibility Score:  5.559
Fsp3:  0.842
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.552
MDCK Permeability:  5.781469553767238e-06
Pgp-inhibitor:  0.003
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.23
30% Bioavailability (F30%):  0.943

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.193
Plasma Protein Binding (PPB):  90.47425079345703%
Volume Distribution (VD):  0.443
Pgp-substrate:  6.264421463012695%

ADMET: Metabolism

CYP1A2-inhibitor:  0.024
CYP1A2-substrate:  0.437
CYP2C19-inhibitor:  0.025
CYP2C19-substrate:  0.779
CYP2C9-inhibitor:  0.102
CYP2C9-substrate:  0.588
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.496
CYP3A4-inhibitor:  0.309
CYP3A4-substrate:  0.075

ADMET: Excretion

Clearance (CL):  5.356
Half-life (T1/2):  0.644

ADMET: Toxicity

hERG Blockers:  0.024
Human Hepatotoxicity (H-HT):  0.599
Drug-inuced Liver Injury (DILI):  0.056
AMES Toxicity:  0.004
Rat Oral Acute Toxicity:  0.104
Maximum Recommended Daily Dose:  0.746
Skin Sensitization:  0.276
Carcinogencity:  0.217
Eye Corrosion:  0.01
Eye Irritation:  0.181
Respiratory Toxicity:  0.944

Download Data

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

  Natural Product: NPC297796

Natural Product ID:  NPC297796
Common Name*:   WMEDLAURVXZWQZ-DGUWLTKGSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  WMEDLAURVXZWQZ-DGUWLTKGSA-N
Standard InCHI:  InChI=1S/C19H28O2/c1-12-4-3-8-18(2)15(12)7-9-19-10-13(5-6-16(18)19)14(11-19)17(20)21/h13-16H,1,3-11H2,2H3,(H,20,21)/t13-,14+,15-,16+,18-,19+/m1/s1
SMILES:  C=C1CCC[C@]2(C)[C@@H]1CC[C@]13C[C@@H](CC[C@@H]23)[C@H](C1)C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0003782] Kaurane diterpenoids

*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
NPO3859 Maytenus magellanica Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[11741484]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota n.a. n.a. n.a. PMID[15679323]
NPO4368 Magnolia officinalis Species Magnoliaceae Eukaryota n.a. n.a. n.a. PMID[1659613]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota roots n.a. n.a. PMID[16643052]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota Roots; Stems; Tubers n.a. n.a. PMID[16872143]
NPO4368 Magnolia officinalis Species Magnoliaceae Eukaryota stem bark n.a. n.a. PMID[17918910]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota roots n.a. n.a. PMID[18452334]
NPO8299 Sorocea muriculata Species Moraceae Eukaryota n.a. root n.a. PMID[18847244]
NPO4368 Magnolia officinalis Species Magnoliaceae Eukaryota Stems; Barks n.a. n.a. PMID[19086868]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota n.a. rhizome n.a. PMID[21902195]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota n.a. tuberous root n.a. PMID[21902195]
NPO4368 Magnolia officinalis Species Magnoliaceae Eukaryota n.a. bark n.a. PMID[23823874]
NPO4368 Magnolia officinalis Species Magnoliaceae Eukaryota n.a. n.a. n.a. PMID[28485933]
NPO473 Artemisia maritima Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4368 Magnolia officinalis Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3599 Rheum maximowiczii Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21651 Cheilocostus speciosus Species Costaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3599 Rheum maximowiczii Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4368 Magnolia officinalis Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO473 Artemisia maritima Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO473 Artemisia maritima Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4368 Magnolia officinalis Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4368 Magnolia officinalis Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8299 Sorocea muriculata Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3021 Arcicella aquatica Species Cytophagaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO4368 Magnolia officinalis Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2479 Dorstenia drakena Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13443 Doris montereyensis Species Dorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO473 Artemisia maritima Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5157 Penstemon nitidus Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4827 Glycyrrhiza macedonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3859 Maytenus magellanica Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1521 Curcuma oligantha Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8419 Lepechinia glomerata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6325 Senecio nebrodensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO787 Lentinus degener Species Lentinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21651 Cheilocostus speciosus Species Costaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7948 Galium sinaicum Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5329 Aspilia bishoplecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5501 Pulicaria angustifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25504 Streptomyces rutgersensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO2887 Ottonia ovata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO3439 Streptomyces koyangensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO3599 Rheum maximowiczii Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19620 Stemona tuberosa Species Stemonaceae 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 NPC297796 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 NPC297796 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