Structure

Physi-Chem Properties

Molecular Weight:  252.17
Volume:  277.901
LogP:  2.14
LogD:  1.791
LogS:  -3.08
# Rotatable Bonds:  5
TPSA:  46.53
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.604
Synthetic Accessibility Score:  4.545
Fsp3:  0.667
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.409
MDCK Permeability:  2.4146647774614394e-05
Pgp-inhibitor:  0.007
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.838
Plasma Protein Binding (PPB):  74.9107666015625%
Volume Distribution (VD):  0.87
Pgp-substrate:  21.27303123474121%

ADMET: Metabolism

CYP1A2-inhibitor:  0.028
CYP1A2-substrate:  0.741
CYP2C19-inhibitor:  0.106
CYP2C19-substrate:  0.879
CYP2C9-inhibitor:  0.03
CYP2C9-substrate:  0.847
CYP2D6-inhibitor:  0.051
CYP2D6-substrate:  0.677
CYP3A4-inhibitor:  0.384
CYP3A4-substrate:  0.529

ADMET: Excretion

Clearance (CL):  4.289
Half-life (T1/2):  0.608

ADMET: Toxicity

hERG Blockers:  0.012
Human Hepatotoxicity (H-HT):  0.088
Drug-inuced Liver Injury (DILI):  0.256
AMES Toxicity:  0.206
Rat Oral Acute Toxicity:  0.048
Maximum Recommended Daily Dose:  0.016
Skin Sensitization:  0.774
Carcinogencity:  0.808
Eye Corrosion:  0.621
Eye Irritation:  0.972
Respiratory Toxicity:  0.472

Download Data

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General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC101583

Natural Product ID:  NPC101583
Common Name*:   WQUKMIHCFQFPQG-BSCSQGBWSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  WQUKMIHCFQFPQG-BSCSQGBWSA-N
Standard InCHI:  InChI=1S/C15H24O3/c1-6-15(5)10-8-13(18-15)11(2)12(16)7-9-14(3,4)17/h6-7,9,11,13,17H,1,8,10H2,2-5H3/b9-7+/t11-,13+,15+/m1/s1
SMILES:  C=C[C@@]1(C)CC[C@@H]([C@H](C)C(=O)/C=C/C(C)(C)O)O1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   12132773
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001967] Oxolanes

*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
NPO15918 Nidema boothii Species Orchidaceae Eukaryota whole plant n.a. n.a. PMID[14987052]
NPO27265 Hopea parviflora Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7892 Paubrasilia echinata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13249 Crudia amazonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14226 Cotyledon orbiculata Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27708 Mythimna separata Species 0ctuidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27304 Stevia sanguinea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27409 Scabiosa atropurpurea Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27155 Aconitum nasutum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27554 Doryanthes palmeri Species Doryanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14097 Verrucosispora gifhornensis Species Micromonosporaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO5306 Infundibulicybe catinus Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27265 Hopea parviflora Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27519 Alternaria chrysanthemi Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27836 Gymnodinium microadriaticum Species Gymnodiniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6164 Lasiosiphon eriocephalus Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27355 Pseudokeronopsis rubra Species Pseudokeronopsidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27227 Matricaria occidentalis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13069 Piper wrightii Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15918 Nidema boothii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27073 Poranthera corymbosa Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2137 Helipterum corymbiflorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7892 Paubrasilia echinata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27447 Yucca aloifolia Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27533 Senecio bergii 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 NPC101583 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 NPC101583 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