Structure

Physi-Chem Properties

Molecular Weight:  344.07
Volume:  308.307
LogP:  -0.408
LogD:  -0.004
LogS:  -1.114
# Rotatable Bonds:  4
TPSA:  184.98
# H-Bond Aceptor:  10
# H-Bond Donor:  7
# Rings:  2
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.256
Synthetic Accessibility Score:  3.902
Fsp3:  0.429
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.374
MDCK Permeability:  8.644159242976457e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.4
Human Intestinal Absorption (HIA):  0.881
20% Bioavailability (F20%):  0.995
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.306
Plasma Protein Binding (PPB):  62.10343933105469%
Volume Distribution (VD):  0.456
Pgp-substrate:  34.38488006591797%

ADMET: Metabolism

CYP1A2-inhibitor:  0.046
CYP1A2-substrate:  0.03
CYP2C19-inhibitor:  0.013
CYP2C19-substrate:  0.043
CYP2C9-inhibitor:  0.008
CYP2C9-substrate:  0.098
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.118
CYP3A4-inhibitor:  0.029
CYP3A4-substrate:  0.008

ADMET: Excretion

Clearance (CL):  2.542
Half-life (T1/2):  0.936

ADMET: Toxicity

hERG Blockers:  0.035
Human Hepatotoxicity (H-HT):  0.044
Drug-inuced Liver Injury (DILI):  0.545
AMES Toxicity:  0.029
Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.004
Skin Sensitization:  0.161
Carcinogencity:  0.007
Eye Corrosion:  0.004
Eye Irritation:  0.225
Respiratory Toxicity:  0.019

Download Data

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

  Natural Product: NPC154816

Natural Product ID:  NPC154816
Common Name*:   WLNGPDPILFYWKF-OAHLLOKOSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  WLNGPDPILFYWKF-OAHLLOKOSA-N
Standard InCHI:  InChI=1S/C15H24/c1-12-7-10-15(11-8-12)13(2)6-5-9-14(15,3)4/h7H,2,5-6,8-11H2,1,3-4H3/t15-/m1/s1
SMILES:  CC1=CC[C@@]2(CC1)C(=C)CCCC2(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   442353
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002517] Chamigranes

*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
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[16562834]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota roots purchased from Kiu Shun Trading Ltd., Vancouver, Canada 2000 PMID[16643021]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. leaf n.a. PMID[17999353]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. rhizome n.a. PMID[18787781]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota Roots; Tubers n.a. n.a. PMID[19639966]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[21302967]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. fruit n.a. PMID[24155209]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[24959987]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[25302569]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25538068]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[27228227]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[27400088]
NPO522 Oenanthe javanica Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[31125231]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[9544564]
NPO19246 Skimmia laureola Species Rutaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO19246 Skimmia laureola Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO522 Oenanthe javanica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23177 Achillea alpina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO542 Artemisia absinthium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8367 Fructus schiandrae n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27984 Achillea moschata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29245 Nepeta leucophylla Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31384 Thuja orientalis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27984 Achillea moschata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29245 Nepeta leucophylla Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO542 Artemisia absinthium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8367 Fructus schiandrae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19246 Skimmia laureola Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23177 Achillea alpina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO522 Oenanthe javanica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO542 Artemisia absinthium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23177 Achillea alpina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27984 Achillea moschata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31384 Thuja orientalis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO522 Oenanthe javanica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO542 Artemisia absinthium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23177 Achillea alpina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO522 Oenanthe javanica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19246 Skimmia laureola Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29245 Nepeta leucophylla Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27984 Achillea moschata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16087 Atractylodes lancea 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 NPC154816 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 NPC154816 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