Structure

Physi-Chem Properties

Molecular Weight:  290.26
Volume:  329.041
LogP:  6.002
LogD:  4.343
LogS:  -5.319
# Rotatable Bonds:  0
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.652
Synthetic Accessibility Score:  5.435
Fsp3:  1.0
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:  -4.771
MDCK Permeability:  1.4221613128029276e-05
Pgp-inhibitor:  0.284
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.9
30% Bioavailability (F30%):  0.98

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.15
Plasma Protein Binding (PPB):  94.99170684814453%
Volume Distribution (VD):  1.468
Pgp-substrate:  3.9964210987091064%

ADMET: Metabolism

CYP1A2-inhibitor:  0.056
CYP1A2-substrate:  0.293
CYP2C19-inhibitor:  0.091
CYP2C19-substrate:  0.883
CYP2C9-inhibitor:  0.22
CYP2C9-substrate:  0.328
CYP2D6-inhibitor:  0.142
CYP2D6-substrate:  0.532
CYP3A4-inhibitor:  0.863
CYP3A4-substrate:  0.235

ADMET: Excretion

Clearance (CL):  9.806
Half-life (T1/2):  0.108

ADMET: Toxicity

hERG Blockers:  0.069
Human Hepatotoxicity (H-HT):  0.547
Drug-inuced Liver Injury (DILI):  0.223
AMES Toxicity:  0.004
Rat Oral Acute Toxicity:  0.448
Maximum Recommended Daily Dose:  0.807
Skin Sensitization:  0.907
Carcinogencity:  0.572
Eye Corrosion:  0.958
Eye Irritation:  0.553
Respiratory Toxicity:  0.935

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  Natural Product: NPC218359

Natural Product ID:  NPC218359
Common Name*:   FZSRMADKTOBCNT-LZHQGQFHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  FZSRMADKTOBCNT-LZHQGQFHSA-N
Standard InCHI:  InChI=1S/C20H34O/c1-17(2)9-5-10-18(3)15(17)8-11-20-12-14(6-7-16(18)20)19(4,21)13-20/h14-16,21H,5-13H2,1-4H3/t14-,15+,16-,18+,19-,20+/m1/s1
SMILES:  CC1(C)CCC[C@@]2(C)[C@H]1CC[C@]13C[C@@H](CC[C@H]23)[C@@](C)(C1)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   101306763
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0003782] Kaurane 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
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]
NPO7904 Ganoderma applanatum Species Polyporaceae Eukaryota n.a. Sri Lankan n.a. PMID[16933889]
NPO5105 Lagenaria siceraria Species Cucurbitaceae Eukaryota n.a. stem n.a. PMID[18310955]
NPO13135 Campylotropis hirtella Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[19481938]
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]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[28294615]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[31291099]
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]
NPO5105 Lagenaria siceraria Species Cucurbitaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO5105 Lagenaria siceraria Species Cucurbitaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4947 Tagetes minuta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6731 Ononis spinosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6454 Delphinium tatsienense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7773 Crinum moorei Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13135 Campylotropis hirtella Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13135 Campylotropis hirtella Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4947 Tagetes minuta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5314 Sargassum parvivesiculosum Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6731 Ononis spinosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7904 Ganoderma applanatum Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7773 Crinum moorei Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6454 Delphinium tatsienense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5105 Lagenaria siceraria Species Cucurbitaceae 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]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12796 Periploca sepium Species Apocynaceae 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]
NPO6731 Ononis spinosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12796 Periploca sepium Species Apocynaceae 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]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2247 Iphiona scabra Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11190 Veronica polita Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12091 Martensia denticulata Species Delesseriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7759 Penicillium nalgiovensis Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10922 Pentaclethra macrophylla Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO526 Salvia sessei Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5043 Eria japonica Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7904 Ganoderma applanatum Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6731 Ononis spinosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1533 Corynespora cassiicola Species Corynesporascaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5105 Lagenaria siceraria Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12205 Eucalyptus apodophylla Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8934 Gypsophila perfoliata Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11576 Glycosmis macrophylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9532 Vernonia cistifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO88 Rheum undulatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13135 Campylotropis hirtella 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]
NPO6289 Ceropegia dichotoma Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3111 Daphnandra micrantha Species Atherospermataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5314 Sargassum parvivesiculosum Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1815 Breonia chinensis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10605 Tristania conferta Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4112 Ficus fistulosa Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5456 Juniperus drupacea Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9704 Sonneratia caseolaris Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22691 Mentha cardiaca Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5260 Osteospermum thodei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7773 Crinum moorei Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23384 Rhodiola semenovii Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6454 Delphinium tatsienense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1257 Distephanus angulifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO421 Polygonum maritimum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4947 Tagetes minuta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10638 Plectranthus myrianthus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2553 Adenocarpus commutatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3873 Crotalaria candicans Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9319 Pterocaulon virgatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5403 Fagus menziesii Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11843 Stephania zippeliana Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7604 Viguiera lanceolata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21720 Talaromyces variabilis Species Trichocomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7822.1 Eucalyptus globulus subsp. bicostata Subspecies Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8197 Scrophularia deserti Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12565 Hypericum polyanthemum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23693 Alseodaphne semecarpifolia Species Lauraceae 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 NPC218359 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 NPC218359 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