Structure

Physi-Chem Properties

Molecular Weight:  576.37
Volume:  587.114
LogP:  3.94
LogD:  3.749
LogS:  -4.571
# Rotatable Bonds:  3
TPSA:  117.84
# H-Bond Aceptor:  8
# H-Bond Donor:  4
# Rings:  7
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.377
Synthetic Accessibility Score:  5.725
Fsp3:  0.939
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -5.005
MDCK Permeability:  1.7879841834655963e-05
Pgp-inhibitor:  0.977
Pgp-substrate:  0.573
Human Intestinal Absorption (HIA):  0.096
20% Bioavailability (F20%):  0.114
30% Bioavailability (F30%):  0.126

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.038
Plasma Protein Binding (PPB):  83.9037094116211%
Volume Distribution (VD):  0.81
Pgp-substrate:  4.381006717681885%

ADMET: Metabolism

CYP1A2-inhibitor:  0.009
CYP1A2-substrate:  0.731
CYP2C19-inhibitor:  0.009
CYP2C19-substrate:  0.359
CYP2C9-inhibitor:  0.017
CYP2C9-substrate:  0.018
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.116
CYP3A4-inhibitor:  0.214
CYP3A4-substrate:  0.143

ADMET: Excretion

Clearance (CL):  6.551
Half-life (T1/2):  0.335

ADMET: Toxicity

hERG Blockers:  0.902
Human Hepatotoxicity (H-HT):  0.236
Drug-inuced Liver Injury (DILI):  0.113
AMES Toxicity:  0.306
Rat Oral Acute Toxicity:  0.063
Maximum Recommended Daily Dose:  0.675
Skin Sensitization:  0.936
Carcinogencity:  0.665
Eye Corrosion:  0.003
Eye Irritation:  0.022
Respiratory Toxicity:  0.978

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Similar NPs/Drugs  

  Natural Product: NPC285044

Natural Product ID:  NPC285044
Common Name*:   WXMARHKAXWRNDM-REQRAIAKSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  WXMARHKAXWRNDM-REQRAIAKSA-N
Standard InCHI:  InChI=1S/C33H52O8/c1-17-7-12-33(38-16-17)18(2)26-24(41-33)14-23-21-6-5-19-13-20(8-10-31(19,3)22(21)9-11-32(23,26)4)39-30-29(37)28(36)27(35)25(15-34)40-30/h5,17-18,20-30,34-37H,6-16H2,1-4H3/t17-,18-,20-,21+,22-,23-,24-,25+,26-,27+,28-,29+,30+,31-,32-,33+/m0/s1
SMILES:  C[C@H]1CC[C@@]2([C@@H](C)[C@H]3[C@H](C[C@H]4[C@@H]5CC=C6C[C@H](CC[C@]6(C)[C@H]5CC[C@]34C)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O)O)O2)OC1
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:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001013] Steroidal glycosides
          • [CHEMONTID:0002364] Steroidal saponins

*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
NPO17509 Gentiana bellidifolia Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0040-4020(01)98434-0]
NPO12113 Aconitum forrestii Species Ranunculaceae Eukaryota n.a. root n.a. DOI[10.1021/np50033a013]
NPO17406 Calophyllum lanigerum Species Calophyllaceae Eukaryota n.a. Sarawak, Malaysia n.a. PMID[11430019]
NPO17406 Calophyllum lanigerum Species Calophyllaceae Eukaryota n.a. n.a. n.a. PMID[1379639]
NPO12900 Sarcococca hookeriana Species Buxaceae Eukaryota n.a. whole plant n.a. PMID[17827771]
NPO14832 Calocedrus macrolepis Species Cupressaceae Eukaryota n.a. leaf n.a. PMID[18206367]
NPO12900 Sarcococca hookeriana Species Buxaceae Eukaryota n.a. n.a. n.a. PMID[18681480]
NPO12900 Sarcococca hookeriana Species Buxaceae Eukaryota n.a. whole plant n.a. PMID[18681480]
NPO19447 Daphniphyllum subverticillatum Species Daphniphyllaceae Eukaryota leaves n.a. n.a. PMID[19739650]
NPO18442 Capsicum baccatum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[21535519]
NPO19581 Marchantia polymorpha Species Marchantiaceae Eukaryota n.a. n.a. n.a. PMID[21625478]
NPO18682 Piper puberulum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[7623032]
NPO17406 Calophyllum lanigerum Species Calophyllaceae Eukaryota n.a. n.a. n.a. PMID[8792623]
NPO8770 Euphorbia wallichii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18608 Fagopyrum cymosum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19581 Marchantia polymorpha Species Marchantiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15880 Microlepia marginata Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18682 Piper puberulum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12113 Aconitum forrestii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16148 Neoboutonia glabrescens Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18682 Piper puberulum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19581 Marchantia polymorpha Species Marchantiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8770 Euphorbia wallichii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12113 Aconitum forrestii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11662 Solanum virginianum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15880 Microlepia marginata Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18608 Fagopyrum cymosum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13433 Adenium obesum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18608 Fagopyrum cymosum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14266 Borassus flabellifer Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22826 Buxus rolfei Species Buxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18361 Mollugo cerviana Species Molluginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17509 Gentiana bellidifolia Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18860 Pelea madagascarica Species Bovidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17406 Calophyllum lanigerum Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18064 Lycopodium paniculatum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19525 Tephrosia bracteolata Species Geometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20860 Lygodium pinnatifidum Species Lygodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18442 Capsicum baccatum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13869 Ranunculus bulbosus Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18940 Selinum papyraceum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2708 Agaricus nebularis Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18540 Berkheya radula Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8770 Euphorbia wallichii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14832 Calocedrus macrolepis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19722 Tephrosia odorata Species Geometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19447 Daphniphyllum subverticillatum Species Daphniphyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18608 Fagopyrum cymosum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18778 Paullinia pinnata Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9099 Carissa spinarum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19098 Hypotrachyna quaesita Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12113 Aconitum forrestii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17793 Parkia javanica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18682 Piper puberulum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16274 Calonectria lauri Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12900 Sarcococca hookeriana Species Buxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13433 Adenium obesum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19314 Albizia schimperana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15183 Salvia horminum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19249 Garcinia latissima Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16148 Neoboutonia glabrescens Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11331 Phellinus tremulae Species Hymenochaetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19842 Sideritis condensata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19581 Marchantia polymorpha Species Marchantiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17648 Subergorgia hicksoni Species Subergorgiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10175 Anaptychia obscura Species Physciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18272 Mikania oblongifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27385 Calamus insignis Species Sparidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19377 Podocarpus blumei Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16571 Canarium muelleri Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11662 Solanum virginianum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15880 Microlepia marginata Species Dennstaedtiaceae 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 NPC285044 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 NPC285044 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