Structure

Physi-Chem Properties

Molecular Weight:  318.22
Volume:  341.348
LogP:  2.648
LogD:  2.104
LogS:  -2.376
# Rotatable Bonds:  0
TPSA:  57.53
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  5
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.675
Synthetic Accessibility Score:  6.168
Fsp3:  0.85
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:  -4.734
MDCK Permeability:  2.202788346039597e-05
Pgp-inhibitor:  0.83
Pgp-substrate:  0.779
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.076

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.779
Plasma Protein Binding (PPB):  77.45600891113281%
Volume Distribution (VD):  1.053
Pgp-substrate:  24.21426773071289%

ADMET: Metabolism

CYP1A2-inhibitor:  0.01
CYP1A2-substrate:  0.539
CYP2C19-inhibitor:  0.029
CYP2C19-substrate:  0.729
CYP2C9-inhibitor:  0.036
CYP2C9-substrate:  0.086
CYP2D6-inhibitor:  0.013
CYP2D6-substrate:  0.147
CYP3A4-inhibitor:  0.897
CYP3A4-substrate:  0.327

ADMET: Excretion

Clearance (CL):  6.767
Half-life (T1/2):  0.641

ADMET: Toxicity

hERG Blockers:  0.012
Human Hepatotoxicity (H-HT):  0.349
Drug-inuced Liver Injury (DILI):  0.048
AMES Toxicity:  0.02
Rat Oral Acute Toxicity:  0.93
Maximum Recommended Daily Dose:  0.687
Skin Sensitization:  0.143
Carcinogencity:  0.635
Eye Corrosion:  0.078
Eye Irritation:  0.149
Respiratory Toxicity:  0.982

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General Info & Identifiers & Properties  
Structure MOL file  
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Similar NPs/Drugs  

  Natural Product: NPC216230

Natural Product ID:  NPC216230
Common Name*:   JHXMMAKVDKZILM-HRPFZTSVSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JHXMMAKVDKZILM-HRPFZTSVSA-N
Standard InCHI:  InChI=1S/C20H30O3/c1-17(2)14-6-8-20-7-5-12(19(4,23)11-20)9-15(20)18(14,3)10-13(21)16(17)22/h5,7,12,14-16,22-23H,6,8-11H2,1-4H3/t12-,14+,15-,16+,18+,19-,20+/m0/s1
SMILES:  CC1(C)[C@H]2CC[C@]34C=C[C@@H](C[C@H]4[C@]2(C)CC(=O)[C@H]1O)[C@](C)(C3)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:0003401] Villanovane, atisane, trachylobane or helvifulvane diterpenoids
            • [CHEMONTID:0002738] Atisane 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
NPO8584 Schisandra arisanensis Species Schisandraceae Eukaryota fruits n.a. n.a. PMID[19673515]
NPO8584 Schisandra arisanensis Species Schisandraceae Eukaryota fruits n.a. n.a. PMID[20536188]
NPO8584 Schisandra arisanensis Species Schisandraceae Eukaryota fruits n.a. n.a. PMID[23265871]
NPO20288 Polytolypa hystricis Species Onygenaceae Eukaryota n.a. n.a. n.a. PMID[8691217]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota Tubers n.a. Database[FooDB]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8584 Schisandra arisanensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19139 Senecio polyodon Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8198 Podocarpus montanus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20846 Sophora japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22294 Pteris inaequalis Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8584 Schisandra arisanensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19139 Senecio polyodon Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15478 Senna sophera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8198 Podocarpus montanus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20846 Sophora japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8198 Podocarpus montanus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20846 Sophora japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20846 Sophora japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22529 Calceolaria thyrsiflora Species Calceolariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20288 Polytolypa hystricis Species Onygenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20846 Sophora japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15478 Senna sophera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20015 Echinocystis lobata Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22711 Athanasia dregeana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22294 Pteris inaequalis Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21530 Arnica viscosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22650 Helenium quadridentatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28627.1 Coptis trifolia subsp. groenlandica Subspecies Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23025 Roccellaria mollis Species Roccellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21822 Berberis crataegina Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8198 Podocarpus montanus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18684 Calophyllum thwaitesii Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22927 Xanthoparmelia pokornyi Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11064 Haemanthus toxicarius Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22812 Acacia cambagei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28078 Melaleuca decora Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21101 Felicia amelloides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19139 Senecio polyodon Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16711 Baccharis solieri Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22599 Crataegus pontica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22871 Aster alpinus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21951 Paramignya griffithii Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23952 Phlomoides medicinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20592 Rhodoglossum japonicum Species Gigartinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8584 Schisandra arisanensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21368 Tricholoma batschii Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23353 [polyangium] brachysporum Species n.a. Bacteria 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 NPC216230 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 NPC216230 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