Structure

Physi-Chem Properties

Molecular Weight:  332.2
Volume:  341.582
LogP:  3.613
LogD:  3.127
LogS:  -4.66
# Rotatable Bonds:  0
TPSA:  44.76
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  5
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.636
Synthetic Accessibility Score:  5.972
Fsp3:  0.85
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -5.185
MDCK Permeability:  2.081509774143342e-05
Pgp-inhibitor:  0.042
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.078
30% Bioavailability (F30%):  0.656

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.122
Plasma Protein Binding (PPB):  76.95958709716797%
Volume Distribution (VD):  1.585
Pgp-substrate:  11.949207305908203%

ADMET: Metabolism

CYP1A2-inhibitor:  0.022
CYP1A2-substrate:  0.831
CYP2C19-inhibitor:  0.292
CYP2C19-substrate:  0.822
CYP2C9-inhibitor:  0.34
CYP2C9-substrate:  0.048
CYP2D6-inhibitor:  0.114
CYP2D6-substrate:  0.076
CYP3A4-inhibitor:  0.921
CYP3A4-substrate:  0.922

ADMET: Excretion

Clearance (CL):  9.84
Half-life (T1/2):  0.541

ADMET: Toxicity

hERG Blockers:  0.274
Human Hepatotoxicity (H-HT):  0.807
Drug-inuced Liver Injury (DILI):  0.636
AMES Toxicity:  0.831
Rat Oral Acute Toxicity:  0.249
Maximum Recommended Daily Dose:  0.917
Skin Sensitization:  0.819
Carcinogencity:  0.956
Eye Corrosion:  0.003
Eye Irritation:  0.031
Respiratory Toxicity:  0.621

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General Info & Identifiers & Properties  
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  Natural Product: NPC296489

Natural Product ID:  NPC296489
Common Name*:   OQLCWZJEAYGVQE-TXWGWWACSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  OQLCWZJEAYGVQE-TXWGWWACSA-N
Standard InCHI:  InChI=1S/C20H28O4/c1-13-11-14-15-17(2,16(21)23-14)5-4-6-18(15,3)20(13)8-7-19(24-20)9-10-22-12-19/h9-10,13-15H,4-8,11-12H2,1-3H3/t13-,14-,15+,17+,18+,19-,20-/m1/s1
SMILES:  C[C@@H]1C[C@@H]2[C@H]3[C@](C)(CCC[C@]3(C)[C@]31CC[C@]1(C=COC1)O3)C(=O)O2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   168199
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000050] Lactones
        • [CHEMONTID:0001245] Gamma butyrolactones

*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
NPO24498 Casearia membranacea Species Salicaceae Eukaryota n.a. leaf n.a. PMID[14709876]
NPO24498 Casearia membranacea Species Salicaceae Eukaryota n.a. twig n.a. PMID[14709876]
NPO24498 Casearia membranacea Species Salicaceae Eukaryota Leaves; Twigs n.a. n.a. PMID[15043402]
NPO23473 Cinnamomum kotoense Species Lauraceae Eukaryota stem wood n.a. n.a. PMID[16180806]
NPO24498 Casearia membranacea Species Salicaceae Eukaryota n.a. n.a. n.a. PMID[16309320]
NPO23473 Cinnamomum kotoense Species Lauraceae Eukaryota leaves n.a. n.a. PMID[16792412]
NPO23769 Ainsliaea macrocephala Species Asteraceae Eukaryota n.a. whole plant n.a. PMID[18484734]
NPO23473 Cinnamomum kotoense Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[18489163]
NPO23557 Zanthoxylum ailanthoides Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[19128011]
NPO24301 Buxus microphylla Species Buxaceae Eukaryota leaves and stems Kunming, Yunnan, China 2007-AUG PMID[19133780]
NPO24498 Casearia membranacea Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24301 Buxus microphylla Species Buxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25037 Nepeta cataria Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23557 Zanthoxylum ailanthoides Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23264 Marrubium vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23302 Strychnos camptoneura Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21478 Buxus hyrcana Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24301 Buxus microphylla Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24498 Casearia membranacea Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23302 Strychnos camptoneura Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23557 Zanthoxylum ailanthoides Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25037 Nepeta cataria Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23264 Marrubium vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24301 Buxus microphylla Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23264 Marrubium vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25037 Nepeta cataria Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24015 Perknaster fuscus Species Ganeriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22684 Enrichment culture Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO24258 Vellozia nivea Species Velloziaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23264 Marrubium vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21352 Boronia ternata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24462 Pityrogramma ebenea Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18918 Lecanicillium muscarium Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28748 Aphis sambuci Species Aphididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23557 Zanthoxylum ailanthoides Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23473 Cinnamomum kotoense Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23930 Luculia pinceana Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24993 Conospermum teretifolium Species Proteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24952 Galeopsis tetrahit Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7197 Colchicum robustum Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18735 Pinus mugo Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25080 Sphaeria maculans n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO23428 Tinus mamillata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO23896 Cytisus ratisbonensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23721 Epidendrum rigidum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21478 Buxus hyrcana Species Buxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23769 Ainsliaea macrocephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20498 Cephalaria ambrosioides Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24301 Buxus microphylla Species Buxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24498 Casearia membranacea Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23474 Abies veitchii Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23849 Dicoma anomala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25037 Nepeta cataria Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23302 Strychnos camptoneura Species Loganiaceae 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 NPC296489 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 NPC296489 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