Structure

Physi-Chem Properties

Molecular Weight:  238.19
Volume:  265.827
LogP:  3.446
LogD:  3.278
LogS:  -2.263
# Rotatable Bonds:  1
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.69
Synthetic Accessibility Score:  4.347
Fsp3:  0.867
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.427
MDCK Permeability:  1.2951681128470227e-05
Pgp-inhibitor:  0.041
Pgp-substrate:  0.848
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.905
30% Bioavailability (F30%):  0.735

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.393
Plasma Protein Binding (PPB):  74.39291381835938%
Volume Distribution (VD):  1.318
Pgp-substrate:  15.202607154846191%

ADMET: Metabolism

CYP1A2-inhibitor:  0.205
CYP1A2-substrate:  0.39
CYP2C19-inhibitor:  0.026
CYP2C19-substrate:  0.852
CYP2C9-inhibitor:  0.072
CYP2C9-substrate:  0.085
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.119
CYP3A4-inhibitor:  0.118
CYP3A4-substrate:  0.5

ADMET: Excretion

Clearance (CL):  15.622
Half-life (T1/2):  0.36

ADMET: Toxicity

hERG Blockers:  0.058
Human Hepatotoxicity (H-HT):  0.398
Drug-inuced Liver Injury (DILI):  0.056
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.904
Maximum Recommended Daily Dose:  0.119
Skin Sensitization:  0.296
Carcinogencity:  0.299
Eye Corrosion:  0.691
Eye Irritation:  0.485
Respiratory Toxicity:  0.953

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  Natural Product: NPC16828

Natural Product ID:  NPC16828
Common Name*:   DGZPYTSARMEKSO-QRTUWBSPSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  DGZPYTSARMEKSO-QRTUWBSPSA-N
Standard InCHI:  InChI=1S/C15H26O2/c1-9(2)11-5-6-15(4,17)13-8-14(16)10(3)7-12(11)13/h7,9,11-14,16-17H,5-6,8H2,1-4H3/t11-,12+,13+,14-,15-/m0/s1
SMILES:  CC(C)[C@@H]1CC[C@@](C)([C@@H]2C[C@@H](C(=C[C@H]12)C)O)O
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:0001550] Sesquiterpenoids

*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
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/0031-9422(81)85171-0]
NPO24559 Cotinus coggygria Species Anacardiaceae Eukaryota Whole plant n.a. n.a. PMID[11141121]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[11514174]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota fruit Hainan Island, China 1998 PMID[12398545]
NPO22375 Saussurea salicifolia Species Asteraceae Eukaryota n.a. aerial part n.a. PMID[18057725]
NPO24900 Vladimiria muliensis n.a. n.a. n.a. n.a. n.a. n.a. PMID[18293903]
NPO24900 Vladimiria muliensis n.a. n.a. n.a. n.a. n.a. n.a. PMID[19432411]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[22277277]
NPO25106 Arnica parryi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23501116]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[23583435]
NPO27031 Methanosarcina barkeri Species Methanosarcinaceae Archaea n.a. n.a. n.a. PMID[24669201]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[25757283]
NPO24843 Pachygone dasycarpa Species Menispermaceae Eukaryota stem bark n.a. n.a. PMID[9157192]
NPO24843 Pachygone dasycarpa Species Menispermaceae Eukaryota n.a. n.a. n.a. PMID[9157192]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1674 Dalbergia nitidula Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24559 Cotinus coggygria Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23547 Strychnos amazonica Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24328 Gratiola officinalis Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29503 Alstonia spectabilis Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23478 Uncaria africana Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24559 Cotinus coggygria Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24328 Gratiola officinalis Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29503 Alstonia spectabilis Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23547 Strychnos amazonica Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23478 Uncaria africana Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1674 Dalbergia nitidula Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23288 Justicia betonica Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24559 Cotinus coggygria Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23547 Strychnos amazonica Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23288 Justicia betonica Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24118 Buxus hildebrandtii Species Buxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24589 Grindelia discoidea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24559 Cotinus coggygria Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29503 Alstonia spectabilis Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21799 Bacillus litoralis Species Bacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO25031 Petunia nyctaginiflora Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24021 Eucryphia cordifolia Species Cunoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22924 Bombus terrestris Species Apidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25068 Zebrina pendula Species Enidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17445 Streptomyces corchorusii Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO27031 Methanosarcina barkeri Species Methanosarcinaceae Archaea n.a. n.a. n.a. Database[UNPD]
NPO21242 Neolitsea villosa Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28259 Viguiera pinnatilobata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23660 Alpinia zerumbet Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23375 Hypericum reptans Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24456 Salvia lavandulifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24191 Drypetes tessmanniana Species Putranjivaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23478 Uncaria africana Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24493 Echinacea simulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27277 Stenocarpella maydis Species Diaporthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18045 Holothuria atra Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24843 Pachygone dasycarpa Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24937 Callicarpa acuminata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24754 Tsitsikamma favus Species Latrunculiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23547 Strychnos amazonica Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25130 Hylotrupes bajulus Species Cerambycidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24813 Agardhiella tenera Species Solieriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25106 Arnica parryi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23750 Escontria chiotilla Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24659 Eremurus chinensis Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24406 Rhizophora tagal Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24688 Streptomyces ramocissimus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO24328 Gratiola officinalis Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23149 Callistemon coccineus Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13455 Hemiselmis virescens Species Hemiselmidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22375 Saussurea salicifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24874 Croton geayi Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23657 Ophiocordyceps heteropoda Species Ophiocordycipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27093 Kniphofia foliosa Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1674 Dalbergia nitidula Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24900 Vladimiria muliensis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO25226 Kalanchoe spathulata Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23837 Rubus laciniatus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19716 Uvaria lucida Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18875 Aconitum contortum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24268 Pteryxia terebinthina Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21483 0nomuraea dietziae Species Streptosporangiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO24969 Ageratum mexicanum Species Asteraceae 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 NPC16828 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 NPC16828 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