Structure

Physi-Chem Properties

Molecular Weight:  480.35
Volume:  508.723
LogP:  4.047
LogD:  4.137
LogS:  -4.349
# Rotatable Bonds:  5
TPSA:  107.22
# H-Bond Aceptor:  6
# H-Bond Donor:  4
# Rings:  4
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.45
Synthetic Accessibility Score:  5.04
Fsp3:  0.964
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.88
MDCK Permeability:  3.6815319617744535e-05
Pgp-inhibitor:  0.995
Pgp-substrate:  0.983
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.862
30% Bioavailability (F30%):  0.861

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.048
Plasma Protein Binding (PPB):  87.8908462524414%
Volume Distribution (VD):  0.91
Pgp-substrate:  3.162703037261963%

ADMET: Metabolism

CYP1A2-inhibitor:  0.076
CYP1A2-substrate:  0.219
CYP2C19-inhibitor:  0.01
CYP2C19-substrate:  0.79
CYP2C9-inhibitor:  0.016
CYP2C9-substrate:  0.075
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.073
CYP3A4-inhibitor:  0.232
CYP3A4-substrate:  0.196

ADMET: Excretion

Clearance (CL):  9.686
Half-life (T1/2):  0.273

ADMET: Toxicity

hERG Blockers:  0.692
Human Hepatotoxicity (H-HT):  0.207
Drug-inuced Liver Injury (DILI):  0.365
AMES Toxicity:  0.036
Rat Oral Acute Toxicity:  0.293
Maximum Recommended Daily Dose:  0.013
Skin Sensitization:  0.87
Carcinogencity:  0.268
Eye Corrosion:  0.068
Eye Irritation:  0.033
Respiratory Toxicity:  0.959

Download Data

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

  Natural Product: NPC231852

Natural Product ID:  NPC231852
Common Name*:   IXVMHGVQKLDRKH-KNBKMWSGSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  IXVMHGVQKLDRKH-KNBKMWSGSA-N
Standard InCHI:  InChI=1S/C28H48O6/c1-14(2)15(3)24(31)25(32)16(4)18-7-8-19-17-13-34-26(33)21-11-22(29)23(30)12-28(21,6)20(17)9-10-27(18,19)5/h14-25,29-32H,7-13H2,1-6H3/t15-,16-,17-,18+,19-,20-,21+,22-,23+,24+,25+,27+,28+/m0/s1
SMILES:  CC(C)[C@H](C)[C@H]([C@@H]([C@@H](C)[C@H]1CC[C@H]2[C@@H]3COC(=O)[C@H]4C[C@@H]([C@@H](C[C@]4(C)[C@H]3CC[C@]12C)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   115196
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001125] Steroid lactones
          • [CHEMONTID:0001774] Brassinolides and derivatives

*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
NPO7904 Ganoderma applanatum Species Polyporaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)91122-1]
NPO88 Rheum undulatum Species Polygonaceae Eukaryota rhizome n.a. n.a. PMID[10714491]
NPO21105 Madhuca longifolia Species Sapotaceae Eukaryota n.a. n.a. n.a. PMID[11141115]
NPO7904 Ganoderma applanatum Species Polyporaceae Eukaryota n.a. Sri Lankan n.a. PMID[16933889]
NPO16139 Garcinia lancilimba Species Clusiaceae Eukaryota n.a. bark n.a. PMID[17541202]
NPO5105 Lagenaria siceraria Species Cucurbitaceae Eukaryota n.a. stem n.a. PMID[18310955]
NPO18438 Samanea saman Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[21228101]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[24176362]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota seeds n.a. n.a. PMID[25466198]
NPO1533 Corynespora cassiicola Species Corynesporascaceae Eukaryota n.a. Xisha Islands coral reef in the South China Sea 2009-DEC PMID[25594263]
NPO1533 Corynespora cassiicola Species Corynesporascaceae Eukaryota n.a. n.a. n.a. PMID[25594263]
NPO7904 Ganoderma applanatum Species Polyporaceae Eukaryota n.a. n.a. n.a. PMID[27996259]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO5105 Lagenaria siceraria Species Cucurbitaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO5105 Lagenaria siceraria Species Cucurbitaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO5105 Lagenaria siceraria Species Cucurbitaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO5105 Lagenaria siceraria Species Cucurbitaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6454 Delphinium tatsienense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4947 Tagetes minuta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19035 Croton cajucara Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7210 Rhizophora mucronata Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4947 Tagetes minuta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6454 Delphinium tatsienense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5314 Sargassum parvivesiculosum Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7904 Ganoderma applanatum Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5105 Lagenaria siceraria Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6454 Delphinium tatsienense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7904 Ganoderma applanatum Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18464 Pilocarpus goudotianus Species Rutaceae Eukaryota n.a. n.a. n.a. Database[Title]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO88 Rheum undulatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2553 Adenocarpus commutatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16088 Streptomyces scabiei Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO4112 Ficus fistulosa Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5403 Fagus menziesii Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6454 Delphinium tatsienense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5260 Osteospermum thodei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8197 Scrophularia deserti Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO421 Polygonum maritimum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2247 Iphiona scabra Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23693 Alseodaphne semecarpifolia Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1856 Tomophagus colossus Species Ganodermataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7210 Rhizophora mucronata Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7904 Ganoderma applanatum Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7604 Viguiera lanceolata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7759 Penicillium nalgiovensis Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21105 Madhuca longifolia Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18464 Pilocarpus goudotianus Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5105 Lagenaria siceraria Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1533 Corynespora cassiicola Species Corynesporascaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20942 Isoplexis isabelliana Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21240 Pinus elliottii Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4947 Tagetes minuta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16139 Garcinia lancilimba Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3111 Daphnandra micrantha Species Atherospermataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13111 Aplophyllum dubium n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO5314 Sargassum parvivesiculosum Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18438 Samanea saman Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO88 Rheum undulatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19035 Croton cajucara Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16994 Codiaeum variegatum Species Euphorbiaceae 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 NPC231852 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 NPC231852 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