Structure

Physi-Chem Properties

Molecular Weight:  424.37
Volume:  488.171
LogP:  6.936
LogD:  5.359
LogS:  -6.597
# Rotatable Bonds:  0
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  5
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.358
Synthetic Accessibility Score:  4.822
Fsp3:  0.9
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.183
MDCK Permeability:  7.70351107348688e-06
Pgp-inhibitor:  0.811
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.015
20% Bioavailability (F20%):  0.977
30% Bioavailability (F30%):  0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.06
Plasma Protein Binding (PPB):  94.70499420166016%
Volume Distribution (VD):  1.28
Pgp-substrate:  1.4348325729370117%

ADMET: Metabolism

CYP1A2-inhibitor:  0.059
CYP1A2-substrate:  0.777
CYP2C19-inhibitor:  0.203
CYP2C19-substrate:  0.97
CYP2C9-inhibitor:  0.212
CYP2C9-substrate:  0.85
CYP2D6-inhibitor:  0.105
CYP2D6-substrate:  0.737
CYP3A4-inhibitor:  0.689
CYP3A4-substrate:  0.764

ADMET: Excretion

Clearance (CL):  5.486
Half-life (T1/2):  0.232

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.384
Drug-inuced Liver Injury (DILI):  0.054
AMES Toxicity:  0.002
Rat Oral Acute Toxicity:  0.129
Maximum Recommended Daily Dose:  0.81
Skin Sensitization:  0.098
Carcinogencity:  0.013
Eye Corrosion:  0.028
Eye Irritation:  0.182
Respiratory Toxicity:  0.966

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  Natural Product: NPC95247

Natural Product ID:  NPC95247
Common Name*:   FXOCQCYCKZXBIJ-PZPDXVKZSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  FXOCQCYCKZXBIJ-PZPDXVKZSA-N
Standard InCHI:  InChI=1S/C30H48O/c1-19-17-24-28(6,21-18-26(2,3)13-9-20(19)21)14-11-23-29(7)16-12-25(31)27(4,5)22(29)10-15-30(23,24)8/h17,19-23H,9-16,18H2,1-8H3/t19-,20-,21+,22-,23+,28-,29-,30+/m0/s1
SMILES:  C[C@H]1C=C2[C@@](C)(CC[C@@H]3[C@@]4(C)CCC(=O)C(C)(C)[C@@H]4CC[C@@]23C)[C@@H]2CC(C)(C)CC[C@@H]12
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:0001552] Sesterterpenoids
          • [CHEMONTID:0002883] Scalarane sesterterpenoids

*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
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[18341288]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[18460139]
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]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota Root 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]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota Roots n.a. Database[FooDB]
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]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8584 Schisandra arisanensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO8198 Podocarpus montanus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
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]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20846 Sophora japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15478 Senna sophera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20846 Sophora japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
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[TM-MC]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29531 Lupinus cosentinii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21951 Paramignya griffithii Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28078 Melaleuca decora Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22529 Calceolaria thyrsiflora Species Calceolariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23025 Roccellaria mollis Species Roccellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16711 Baccharis solieri Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20846 Sophora japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22871 Aster alpinus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20015 Echinocystis lobata Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2161 Strychnos ledermannii Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22294 Pteris inaequalis Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22650 Helenium quadridentatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13123 Balanophora harlandii Species Balanophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO245 Euphorbia biglandulosa Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22927 Xanthoparmelia pokornyi Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20592 Rhodoglossum japonicum Species Gigartinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21822 Berberis crataegina Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22812 Acacia cambagei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8198 Podocarpus montanus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1584 Tolypothrix tjipanasensis Species Tolypothrichaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO19139 Senecio polyodon Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18684 Calophyllum thwaitesii Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22599 Crataegus pontica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23952 Phlomoides medicinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20288 Polytolypa hystricis Species Onygenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15478 Senna sophera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11064 Haemanthus toxicarius Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8584 Schisandra arisanensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22711 Athanasia dregeana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21368 Tricholoma batschii Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21530 Arnica viscosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21101 Felicia amelloides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17549 Polemonium caeruleum Species Polemoniaceae 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]
NPO513 Agathosma scaberula Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4892 Viburnum davidii Species Adoxaceae 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 NPC95247 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 NPC95247 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