Structure

Physi-Chem Properties

Molecular Weight:  346.14
Volume:  342.513
LogP:  1.081
LogD:  0.561
LogS:  -3.971
# Rotatable Bonds:  0
TPSA:  97.74
# H-Bond Aceptor:  6
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.399
Synthetic Accessibility Score:  5.838
Fsp3:  0.684
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.2
MDCK Permeability:  4.99501584272366e-05
Pgp-inhibitor:  0.014
Pgp-substrate:  0.384
Human Intestinal Absorption (HIA):  0.034
20% Bioavailability (F20%):  0.169
30% Bioavailability (F30%):  0.776

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.061
Plasma Protein Binding (PPB):  65.45304870605469%
Volume Distribution (VD):  0.325
Pgp-substrate:  32.15993881225586%

ADMET: Metabolism

CYP1A2-inhibitor:  0.022
CYP1A2-substrate:  0.42
CYP2C19-inhibitor:  0.023
CYP2C19-substrate:  0.826
CYP2C9-inhibitor:  0.018
CYP2C9-substrate:  0.106
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.07
CYP3A4-inhibitor:  0.569
CYP3A4-substrate:  0.421

ADMET: Excretion

Clearance (CL):  5.137
Half-life (T1/2):  0.812

ADMET: Toxicity

hERG Blockers:  0.035
Human Hepatotoxicity (H-HT):  0.274
Drug-inuced Liver Injury (DILI):  0.737
AMES Toxicity:  0.039
Rat Oral Acute Toxicity:  0.099
Maximum Recommended Daily Dose:  0.011
Skin Sensitization:  0.777
Carcinogencity:  0.04
Eye Corrosion:  0.052
Eye Irritation:  0.08
Respiratory Toxicity:  0.853

Download Data

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

  Natural Product: NPC189642

Natural Product ID:  NPC189642
Common Name*:   PKCDREAJEQQORV-OTOVEGKDSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PKCDREAJEQQORV-OTOVEGKDSA-N
Standard InCHI:  InChI=1S/C19H22O6/c1-7-5-10(20)16(23)18(3)9(7)6-11(21)19(4)12-8(2)14(25-17(12)24)13(22)15(18)19/h5-6,8,12-16,22-23H,1-4H3/t8-,12-,13+,14-,15+,16-,18+,19+/m1/s1
SMILES:  CC1=CC(=O)[C@H]([C@@]2(C)C1=CC(=O)[C@@]1(C)[C@@H]3[C@@H](C)[C@H]([C@@H]([C@@H]21)O)OC3=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:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001125] Steroid lactones

*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
NPO14602 Vitex negundo Species Lamiaceae Eukaryota leaves n.a. n.a. PMID[12828478]
NPO9965 Eurycoma longifolia Species Simaroubaceae Eukaryota Roots n.a. n.a. PMID[14575431]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota n.a. root n.a. PMID[15520511]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota seeds n.a. n.a. PMID[15620254]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota seeds n.a. n.a. PMID[1624939]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17027268]
NPO9965 Eurycoma longifolia Species Simaroubaceae Eukaryota n.a. root n.a. PMID[1800638]
NPO9965 Eurycoma longifolia Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO9965 Eurycoma longifolia Species Simaroubaceae Eukaryota roots n.a. n.a. PMID[19299148]
NPO11530 Heterosigma akashiwo Species Chattonellaceae Eukaryota n.a. n.a. n.a. PMID[19659728]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota Seeds n.a. n.a. PMID[19715321]
NPO9965 Eurycoma longifolia Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[19919052]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota Seeds n.a. n.a. PMID[19931461]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23403897]
NPO9965 Eurycoma longifolia Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[24467387]
NPO9965 Eurycoma longifolia Species Simaroubaceae Eukaryota roots n.a. n.a. PMID[25066952]
NPO9965 Eurycoma longifolia Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[25905468]
NPO5401 Monanchora unguiculata Species Crambeidae Eukaryota n.a. n.a. n.a. PMID[28368118]
NPO9644 Euphorbia resinifera Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[29667820]
NPO9965 Eurycoma longifolia Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9644 Euphorbia resinifera Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9644 Euphorbia resinifera Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9965 Eurycoma longifolia Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO893 Helichrysum sutherlandii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9644 Euphorbia resinifera Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9024 Aralidium pinnatifidum Species Torricelliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8640 Nemuaron humboldtii Species Atherospermataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8820 Lophocereus marginatus Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13604 Dermocybe cardinalis Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8220 Russula sardonia Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1418 Boletinus paluster Species Gyrodontaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12577 Pinus glauca Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13692 Leontice kiangnanensis Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2084 Acinetobacter calcoaceticus Species Moraxellaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12988 Blainvillea latifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6626 Pteris spinulosa Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14602 Vitex negundo Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20318 Acinetobacter baumannii Species Moraxellaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12026 Papaver radicatum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5401 Monanchora unguiculata Species Crambeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2505 Pachycereus pringlei Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11072 Geigeria schinzii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20383 Stenocereus thurberi Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9375 Medium grandiflorum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO6014 Goniothalamus undulatus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14280 Helichrysum angustifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3576 Bersama swinnyi Species Melianthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO893 Helichrysum sutherlandii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13494 Prosopis kuntzei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3924 Penicillium alutaceum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13798 Cheilanthes marantae Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11530 Heterosigma akashiwo Species Chattonellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22888 Lophiostoma vaginatispora Species Lophiostomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9965 Eurycoma longifolia Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12890 Ophryosporus charua 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 NPC189642 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 NPC189642 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