Structure

Physi-Chem Properties

Molecular Weight:  432.32
Volume:  459.37
LogP:  4.975
LogD:  4.419
LogS:  -4.681
# Rotatable Bonds:  0
TPSA:  58.92
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  6
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.579
Synthetic Accessibility Score:  5.454
Fsp3:  1.0
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:  -4.785
MDCK Permeability:  2.1602269043796696e-05
Pgp-inhibitor:  0.994
Pgp-substrate:  0.997
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.087
30% Bioavailability (F30%):  0.416

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.411
Plasma Protein Binding (PPB):  78.96834564208984%
Volume Distribution (VD):  1.515
Pgp-substrate:  5.32797908782959%

ADMET: Metabolism

CYP1A2-inhibitor:  0.04
CYP1A2-substrate:  0.546
CYP2C19-inhibitor:  0.024
CYP2C19-substrate:  0.816
CYP2C9-inhibitor:  0.088
CYP2C9-substrate:  0.023
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.254
CYP3A4-inhibitor:  0.306
CYP3A4-substrate:  0.25

ADMET: Excretion

Clearance (CL):  12.688
Half-life (T1/2):  0.271

ADMET: Toxicity

hERG Blockers:  0.977
Human Hepatotoxicity (H-HT):  0.407
Drug-inuced Liver Injury (DILI):  0.485
AMES Toxicity:  0.031
Rat Oral Acute Toxicity:  0.336
Maximum Recommended Daily Dose:  0.849
Skin Sensitization:  0.964
Carcinogencity:  0.325
Eye Corrosion:  0.794
Eye Irritation:  0.211
Respiratory Toxicity:  0.961

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  Natural Product: NPC24106

Natural Product ID:  NPC24106
Common Name*:   BQNMOLSYHYSCMS-TUUYSWIFSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  BQNMOLSYHYSCMS-TUUYSWIFSA-N
Standard InCHI:  InChI=1S/C27H44O4/c1-15-7-10-27(30-14-15)16(2)24-22(31-27)12-21-19-6-5-17-11-18(28)8-9-25(17,3)20(19)13-23(29)26(21,24)4/h15-24,28-29H,5-14H2,1-4H3/t15-,16+,17+,18+,19-,20+,21+,22+,23-,24+,25+,26-,27-/m1/s1
SMILES:  C[C@@H]1CC[C@@]2([C@@H](C)[C@H]3[C@H](C[C@H]4[C@@H]5CC[C@H]6C[C@H](CC[C@]6(C)[C@H]5C[C@H]([C@]34C)O)O)O2)OC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   167555
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

*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
NPO19920 Yucca gloriosa Species Asparagaceae Eukaryota n.a. stem n.a. DOI[10.1016/0031-9422(89)80212-2]
NPO10574 Machilus thunbergii Species Lauraceae Eukaryota n.a. bark n.a. PMID[11045899]
NPO21106 Isatis costata Species Brassicaceae Eukaryota n.a. whole plant n.a. PMID[17846565]
NPO10574 Machilus thunbergii Species Lauraceae Eukaryota n.a. bark n.a. PMID[19555186]
NPO19108 Arthrinium sacchari Species Apiosporaceae Eukaryota n.a. n.a. n.a. PMID[21718054]
NPO22631 Actinopolyspora erythraea Species Actinopolysporaceae Bacteria n.a. mycelium n.a. PMID[21870828]
NPO21735 Clausena anisum-olens Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[28368606]
NPO21635 Pandalus borealis Species Pandalidae Eukaryota n.a. n.a. n.a. PMID[3349210]
NPO22060 Hippomane mancinella Species Euphorbiaceae Eukaryota Latex n.a. n.a. PMID[6481361]
NPO19070 Cassia dentata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20952 Dioscorea cirrhosa Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10574 Machilus thunbergii Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22060 Hippomane mancinella Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22578 Speranskia tuberculata Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19070 Cassia dentata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22578 Speranskia tuberculata Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22060 Hippomane mancinella Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20952 Dioscorea cirrhosa Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10574 Machilus thunbergii Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19070 Cassia dentata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20032 Prunus sibirica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20182 Euonymus pendulus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22187 Ostrea virginica Species Ostreidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20952 Dioscorea cirrhosa Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18568 Artemisia aucheri Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22993 Veronica hederifolia Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10574 Machilus thunbergii Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21735 Clausena anisum-olens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22938 Genista hystrix Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21997 Benzoin trilobum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO20042 Ambrosia cumanensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23094 Pectinophora gossypiella Species Gelechiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20032 Prunus sibirica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23475 Psoralea acaulis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22453 Befaria racemosa n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO17819 Ferula transiliensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19108 Arthrinium sacchari Species Apiosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21635 Pandalus borealis Species Pandalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22578 Speranskia tuberculata Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22321 Euphorbia lamprocarpa Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25227 Senecio roseus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23176 Schefflera bodinieri Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20358 Streptomyces maritimus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO15934 Rhododendron ponticum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22060 Hippomane mancinella Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9972 Angostura granulosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19920 Yucca gloriosa Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22119 Echinops bannaticus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14364 Alisma plantago-aquatica Species Alismataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27833 Xerotus discolor Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22881 Cryptotermes brevis Species Termitoidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22697 Licaria mahuba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19380 Styela plicata Species Styelidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7217 Plakobranchus ocellatus Species Placobranchidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17898 Buckiella undulata Species Hypnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21246 Helichrysum anomalum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20506 Batatas edulis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO21106 Isatis costata Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19693 Lobaria oregana Species Lobariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17092 Viguiera dentata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14211 Acinetobacter junii Species Moraxellaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO5927 Cortinarius venetus Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23056 Isaria japonica Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19070 Cassia dentata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22631 Actinopolyspora erythraea Species Actinopolysporaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO23133 Gypsophila patrini Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20677 Fraxinus angustifolia Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12005 Amomum zambesiacum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18197 Cadlina luteomarginata Species Chromodorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21874 Cercospora melonis Species Mycosphaerellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22246 Aplidium longithorax Species Polyclinidae 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 NPC24106 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 NPC24106 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