Structure

Physi-Chem Properties

Molecular Weight:  204.19
Volume:  239.69
LogP:  5.552
LogD:  4.796
LogS:  -5.284
# Rotatable Bonds:  1
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.559
Synthetic Accessibility Score:  5.199
Fsp3:  0.867
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:  -4.26
MDCK Permeability:  1.9259841792518273e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.853
30% Bioavailability (F30%):  0.729

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.113
Plasma Protein Binding (PPB):  95.72028350830078%
Volume Distribution (VD):  2.783
Pgp-substrate:  3.862860679626465%

ADMET: Metabolism

CYP1A2-inhibitor:  0.873
CYP1A2-substrate:  0.329
CYP2C19-inhibitor:  0.261
CYP2C19-substrate:  0.894
CYP2C9-inhibitor:  0.256
CYP2C9-substrate:  0.075
CYP2D6-inhibitor:  0.025
CYP2D6-substrate:  0.264
CYP3A4-inhibitor:  0.437
CYP3A4-substrate:  0.416

ADMET: Excretion

Clearance (CL):  19.949
Half-life (T1/2):  0.173

ADMET: Toxicity

hERG Blockers:  0.102
Human Hepatotoxicity (H-HT):  0.226
Drug-inuced Liver Injury (DILI):  0.451
AMES Toxicity:  0.013
Rat Oral Acute Toxicity:  0.698
Maximum Recommended Daily Dose:  0.036
Skin Sensitization:  0.645
Carcinogencity:  0.24
Eye Corrosion:  0.962
Eye Irritation:  0.628
Respiratory Toxicity:  0.914

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General Info & Identifiers & Properties  
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Similar NPs/Drugs  

  Natural Product: NPC34258

Natural Product ID:  NPC34258
Common Name*:   VLXDPFLIRFYIME-QRTUWBSPSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VLXDPFLIRFYIME-QRTUWBSPSA-N
Standard InCHI:  InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11-,12+,13+,14-,15-/m0/s1
SMILES:  CC(C)[C@@H]1CC[C@@]2(C)[C@@H]3CC=C(C)[C@H]2[C@H]13
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   20055075
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
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. leaf n.a. DOI[10.1007/s11418-006-0112-9]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. stem n.a. DOI[10.1007/s11418-006-0112-9]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. flower n.a. DOI[10.1007/s11418-006-0112-9]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Flower buds n.a. n.a. PMID[12880307]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. root n.a. PMID[17238120]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Stems n.a. n.a. PMID[17663584]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[18177011]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Roots n.a. n.a. PMID[18186611]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. root n.a. PMID[18405608]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. root n.a. PMID[18661821]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[19271742]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[20590154]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21417376]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21627108]
NPO18454 Ligularia hodgsonii Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22642381]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Steamed Roots n.a. n.a. PMID[26200131]
NPO2722 Humulus japonicus Species Cannabaceae Eukaryota Aerial Parts n.a. n.a. PMID[29254897]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. PMID[6387056]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. root n.a. PMID[7700984]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[8064299]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[8064299]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Resin, Exudate, Sap n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Rhizome n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO23197 Juniperus oxycedrus Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2722 Humulus japonicus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2722 Humulus japonicus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23197 Juniperus oxycedrus Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2722 Humulus japonicus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21769 Pterocarpus dalbergioides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25636 Bunium paucifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2722 Humulus japonicus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17193 Picridium crystallinum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17284 Bidens andicola Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23029 Tetradenia riparia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22349 Cucumaria frondosa Species Cucumariidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18454 Ligularia hodgsonii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19830 Chamonixia caespitosa Species Boletaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20157 Boykinia tellimoides Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21902 Thalictrum sachalinense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23197 Juniperus oxycedrus Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13434 Acremonium furcatum Species Plectosphaerellaceae 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 NPC34258 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 NPC34258 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