Structure

Physi-Chem Properties

Molecular Weight:  427.31
Volume:  456.304
LogP:  3.898
LogD:  4.164
LogS:  -4.406
# Rotatable Bonds:  0
TPSA:  58.56
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  6
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.567
Synthetic Accessibility Score:  5.638
Fsp3:  0.889
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:  -4.969
MDCK Permeability:  1.0263946933264378e-05
Pgp-inhibitor:  0.308
Pgp-substrate:  0.997
Human Intestinal Absorption (HIA):  0.208
20% Bioavailability (F20%):  0.899
30% Bioavailability (F30%):  0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.653
Plasma Protein Binding (PPB):  76.73246002197266%
Volume Distribution (VD):  1.85
Pgp-substrate:  8.266556739807129%

ADMET: Metabolism

CYP1A2-inhibitor:  0.024
CYP1A2-substrate:  0.236
CYP2C19-inhibitor:  0.078
CYP2C19-substrate:  0.915
CYP2C9-inhibitor:  0.059
CYP2C9-substrate:  0.048
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.869
CYP3A4-inhibitor:  0.829
CYP3A4-substrate:  0.568

ADMET: Excretion

Clearance (CL):  12.495
Half-life (T1/2):  0.296

ADMET: Toxicity

hERG Blockers:  0.859
Human Hepatotoxicity (H-HT):  0.351
Drug-inuced Liver Injury (DILI):  0.594
AMES Toxicity:  0.03
Rat Oral Acute Toxicity:  0.692
Maximum Recommended Daily Dose:  0.91
Skin Sensitization:  0.293
Carcinogencity:  0.522
Eye Corrosion:  0.004
Eye Irritation:  0.011
Respiratory Toxicity:  0.963

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  Natural Product: NPC238829

Natural Product ID:  NPC238829
Common Name*:   KYELXPJVGNZIGC-GKFGJCLESA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  KYELXPJVGNZIGC-GKFGJCLESA-N
Standard InCHI:  InChI=1S/C27H41NO3/c1-14-9-24-25(28-13-14)16(3)27(31-24)8-6-18-19(15(27)2)11-21-20(18)12-23(30)22-10-17(29)5-7-26(21,22)4/h14,16-18,20-22,24-25,28-29H,5-13H2,1-4H3/p+1/t14-,16+,17-,18+,20-,21-,22+,24+,25-,26+,27-/m0/s1
SMILES:  C[C@H]1C[C@@H]2[C@H]([C@@H](C)[C@@]3(CC[C@@H]4C(=C3C)C[C@H]3[C@H]4CC(=O)[C@H]4C[C@H](CC[C@]34C)O)O2)[NH2+]C1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   161294
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0002724] Steroidal alkaloids
          • [CHEMONTID:0002728] Jerveratrum-type alkaloids

*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
NPO10290.1 Fritillaria ebeiensis var. purpurea Varieties Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18644 Fritillaria walujewii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11228 Fritillaria pallidiflora Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22292 Fritillaria przewalskii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1279 Fritillaria cirrhosa Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12867 Fritillaria siechuanica Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25808.1 Fritillaria taipaiensis var. ningxiaensis Varieties Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7844 Fritillaria hupehensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12273 Fritillaria delavayi Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14849 Fritillaria unibracteata Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10290 Fritillaria ebeiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14347 Fritillaria anhuiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11228 Fritillaria pallidiflora Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10290 Fritillaria ebeiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14347 Fritillaria anhuiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14849 Fritillaria unibracteata Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25334 Bulbus fritillariae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO22292 Fritillaria przewalskii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12867 Fritillaria siechuanica Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18644 Fritillaria walujewii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25808.1 Fritillaria taipaiensis var. ningxiaensis Varieties Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7844 Fritillaria hupehensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10290.1 Fritillaria ebeiensis var. purpurea Varieties Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12273 Fritillaria delavayi Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1279 Fritillaria cirrhosa Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12273 Fritillaria delavayi Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22292 Fritillaria przewalskii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18644 Fritillaria walujewii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14347 Fritillaria anhuiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11228 Fritillaria pallidiflora Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14849 Fritillaria unibracteata Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12556 Fritillaria verticillata Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18644 Fritillaria walujewii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22292 Fritillaria przewalskii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12556 Fritillaria verticillata Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1279 Fritillaria cirrhosa Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25808 Fritillaria taipaiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12273 Fritillaria delavayi Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11228 Fritillaria pallidiflora Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14135 Fritillaria prezewalskii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7844 Fritillaria hupehensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14849 Fritillaria unibracteata Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4487 Fritillaria thunbergii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25941 Garcinia yunnanensis Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26065 Elaeocarpus archboldianus Species Elaeocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1279 Fritillaria cirrhosa Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12556 Fritillaria verticillata Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25808 Fritillaria taipaiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26340 Chione venosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26765 Litsea pedunculata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10290 Fritillaria ebeiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12273 Fritillaria delavayi Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26282 Phebalium ovatifolium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1158 Isochrysis galbana Species Isochrysidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25749 Kielmeyera argentea Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4487 Fritillaria thunbergii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14347 Fritillaria anhuiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11228 Fritillaria pallidiflora Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14849 Fritillaria unibracteata Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22292 Fritillaria przewalskii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25253 Corydalis caseana Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18644 Fritillaria walujewii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26833 Ichnocarpus frutescens Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25300 Senecio ruderalis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7844 Fritillaria hupehensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28973 Rhytisma fulvum Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26096 Jatropha multiloba Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23477 Anabaena torulosa Species 0stocaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO5648 Fritillaria ussuriensis Species Liliaceae 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 NPC238829 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 NPC238829 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