Structure

Physi-Chem Properties

Molecular Weight:  238.19
Volume:  265.827
LogP:  2.078
LogD:  2.379
LogS:  -2.093
# Rotatable Bonds:  1
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.69
Synthetic Accessibility Score:  4.267
Fsp3:  0.867
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:  -4.632
MDCK Permeability:  1.4928657947166357e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.024
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.116
30% Bioavailability (F30%):  0.01

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.051
Plasma Protein Binding (PPB):  67.8899917602539%
Volume Distribution (VD):  1.124
Pgp-substrate:  27.06536102294922%

ADMET: Metabolism

CYP1A2-inhibitor:  0.026
CYP1A2-substrate:  0.208
CYP2C19-inhibitor:  0.02
CYP2C19-substrate:  0.782
CYP2C9-inhibitor:  0.057
CYP2C9-substrate:  0.221
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.162
CYP3A4-inhibitor:  0.036
CYP3A4-substrate:  0.211

ADMET: Excretion

Clearance (CL):  5.554
Half-life (T1/2):  0.295

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.117
Drug-inuced Liver Injury (DILI):  0.03
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.058
Maximum Recommended Daily Dose:  0.802
Skin Sensitization:  0.258
Carcinogencity:  0.08
Eye Corrosion:  0.925
Eye Irritation:  0.96
Respiratory Toxicity:  0.674

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  Natural Product: NPC39620

Natural Product ID:  NPC39620
Common Name*:   LEEZDPXWPYCRRM-COMQUAJESA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LEEZDPXWPYCRRM-COMQUAJESA-N
Standard InCHI:  InChI=1S/C15H26O2/c1-10-12-9-11(14(2,3)17)5-7-15(12,4)8-6-13(10)16/h11-13,16-17H,1,5-9H2,2-4H3/t11-,12+,13-,15+/m1/s1
SMILES:  C=C1[C@@H]2C[C@@H](CC[C@@]2(C)CC[C@H]1O)C(C)(C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11118126
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0000101] Eudesmane, isoeudesmane or cycloeudesmane 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
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11746-997-0093-1]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. Wrocław, Poland 2004–2005 DOI[10.1016/J.FOODCHEM.2006.08.014]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.1016/j.foodchem.2009.03.042]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/jf950732o]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/jf980687v]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.3136/fstr.15.499]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.5897/AJB10.140]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.5897/AJB2010.000-3252]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.5897/JMPR.9000078]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[10775096]
NPO26919 Sanguisorba officinalis Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[11520216]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. flower n.a. PMID[12130858]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. root n.a. PMID[1622242]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[16659156]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[16668466]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[20963508]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO22437 Eurya japonica Species Pentaphylacaceae Eukaryota n.a. n.a. n.a. PMID[23540981]
NPO7635 Glycine max Species Fabaceae Eukaryota Seeds Tekirdag, Turkey PMID[24499198]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers Tongxiang, China n.a. PMID[24621197]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25053043]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25070365]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. seed n.a. PMID[25369450]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25369450]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[26099993]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota Flowers n.a. n.a. PMID[28156114]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. PMID[28248102]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[29400471]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota Aerial Parts n.a. n.a. PMID[30726671]
NPO30745 Chrysanthemum morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[8158164]
NPO30745 Chrysanthemum morifolium Species Asteraceae Eukaryota n.a. inflorescence n.a. PMID[8158164]
NPO7635 Glycine max Species Fabaceae Eukaryota Cotyledon n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Hypocotyl n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Testa n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO30745 Chrysanthemum morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22437 Eurya japonica Species Pentaphylacaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26919 Sanguisorba officinalis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO183 Rhododendron simsii Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22578 Speranskia tuberculata Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31547 Chaenomeles lagenaria Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. seed n.a. Database[MetaboLights]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO7635 Glycine max Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3813 Chaenomeles speciosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO183 Rhododendron simsii Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22578 Speranskia tuberculata Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22437 Eurya japonica Species Pentaphylacaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26919 Sanguisorba officinalis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO183 Rhododendron simsii Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26919 Sanguisorba officinalis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3813 Chaenomeles speciosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30745 Chrysanthemum morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31547 Chaenomeles lagenaria Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3813 Chaenomeles speciosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26919 Sanguisorba officinalis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26919 Sanguisorba officinalis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO183 Rhododendron simsii Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3813 Chaenomeles speciosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22578 Speranskia tuberculata Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22437 Eurya japonica Species Pentaphylacaceae 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 NPC39620 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 NPC39620 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